Transcription factor Sp1 prevents TRF2(ΔBΔM)-induced premature senescence in human diploid fibroblasts.

Telomere uncapping is thought to be the fundamental cause of replicative cellular senescence, but the cellular machineries mediating this process have not been fully understood. In the present study, we present the role of Sp1 transcription factor in the state of telomere uncapping using the TRF2(ΔBΔM)-induced senescence model in human diploid fibroblasts. We observed that the expression of Sp1 is down-regulated in the TRF2(ΔBΔM)-induced senescence, which was mediated by ATM and p38 MAPK. In addition, overexpression of Sp1 prevented the TRF2(ΔBΔM)-induced senescence. Among transcriptional targets of Sp1, expression levels of nuclear transport genes such as karyopherin α, Nup107, and Nup50 were down-regulated in the TRF2(ΔBΔM)-induced senescence, which was prevented by Sp1 overexpression. Moreover, inhibition of the nuclear transport by wheat germ agglutinin (an import inhibitor) and leptomycin B (an export inhibitor) induced premature senescence. These results suggest that Sp1 is an anti-senescence transcription factor in the telomere uncapping-induced senescence and that down-regulation of Sp1 leads to the senescence via down-regulation of the nuclear transport.

The PP2A regulatory subunit Tap46, a component of the TOR signaling pathway, modulates growth and metabolism in plants.

Tap42/α4, a regulatory subunit of protein phosphatase 2A, is a downstream effector of the target of rapamycin (TOR) protein kinase, which regulates cell growth in coordination with nutrient and environmental conditions in yeast and mammals. In this study, we characterized the functions and phosphatase regulation of plant Tap46. Depletion of Tap46 resulted in growth arrest and acute plant death with morphological markers of programmed cell death. Tap46 interacted with PP2A and PP2A-like phosphatases PP4 and PP6. Tap46 silencing modulated cellular PP2A activities in a time-dependent fashion similar to TOR silencing. Immunoprecipitated full-length and deletion forms of Arabidopsis thaliana TOR phosphorylated recombinant Tap46 protein in vitro, supporting a functional link between Tap46 and TOR. Tap46 depletion reproduced the signature phenotypes of TOR inactivation, such as dramatic repression of global translation and activation of autophagy and nitrogen mobilization, indicating that Tap46 may act as a positive effector of TOR signaling in controlling those processes. Additionally, Tap46 silencing in tobacco (Nicotiana tabacum) BY-2 cells caused chromatin bridge formation at anaphase, indicating its role in sister chromatid segregation. These findings suggest that Tap46, in conjunction with associated phosphatases, plays an essential role in plant growth and development as a component of the TOR signaling pathway.

Draft genome for Pseudomonas alkylphenolica IMGN1, isolated from soil.

Biocontrol using organisms like Pseudomonas alkylphenolica offers a viable alternative to chemical pesticides, enhancing plant growth and reducing environmental impact. This study details the genome of Pseudomonas alkylphenolica IMGN1, a strain known for promoting plant growth, advancing our understanding of biocontrol mechanisms.

Complete genome sequence of Bacillus paramobilis sp. strain IMGN7 from soil.

Here, we report the complete genome sequence of Bacillus paramobilis sp. strain IMGN7, which was isolated from soil in South Korea. Its complete genome size is 5.28 Mbp. This genome will provide various insights for further studies about their function as biocontrol agents, such as bioremediation and antibiosis.

Draft genome sequence of Priestia megaterium strain IMGN3 derived from soil.

Priestia megaterium sp. strain IMGN3 was isolated from the soil in South Korea. Here, we report its draft genome sequence, comprising 12 contigs with a total sequence length of 5.64 Mbp. This genome will provide valuable resources for future genomic studies, particularly focusing on plant growth promotion and biocontrol.

Complete genome sequence of Pseudomonas fluorescens IMGN2 isolated from undisturbed soil.

Here, we report the complete genome sequence of Pseudomonas fluorescens IMGN2, highlighting its biocontrol and plant growth-promoting capabilities. The genome analysis reveals genetic features that contribute to its potential in agricultural biotechnology, including genes related to secondary metabolite synthesis and plant-microbe interactions.

Complete genome sequence of bacterium Peribacillus simplex strain IMGN11 from soil.

We report the complete genome sequence of Peribacillus simplex, a spore-forming bacterium originally classified within the Bacillus genus. Peribacillus simplex exhibits antibiotic, plant growth-promoting, and xenobiotic-degrading activities and resistance to environmental contamination. The genome sequence of Peribacillus simplex will provide insights into its capabilities and potential as a biocontrol agent.

Draft genome sequence of bacterium Bacillus proteolyticus strain IMGN4 from soil.

Here, we present the draft genome of Bacillus proteolyticus IMGN4, the gram-positive, soil-dwelling bacterium discovered in mountain Maemi, Republic of Korea in May 2019. The assembly resulted in 7 contigs, comprising a total of 6,063,502 base pairs and have 6,115 coding sequences.

Characterization of in vivo functions of Nicotiana benthamiana RabE1.

We characterized the gene expression, subcellular localization, and in vivo functions of a Nicotiana benthamiana small GTPase belonging to the RabE family, designated NbRabE1. The NbRabE1 promoter drove strong ß-glucuronidase reporter expression in young tissues containing actively dividing cells and in stomata guard cells. GFP fusion proteins of NbRabE1 and its dominant-negative and constitutively active mutants were all localized to the Golgi apparatus and the plasma membrane but showed different affinities for membrane attachment. Virus-induced gene silencing of NbRabE1 resulted in pleiotropic phenotypes, including growth arrest, premature senescence, and abnormal leaf development. At the cellular level, the leaves in which NbRabE1 was silenced contained abnormal stomata that lacked pores or contained incomplete ventral walls, suggesting that NbRabE1 deficiency leads to defective guard cell cytokinesis. Ectopic expression of the dominant-negative mutant of NbRabE1 in Arabidopsis thaliana resulted in retardation of shoot and root growth accompanied by defective root hair formation. These developmental defects are discussed in conjunction with proposed functions of RabE GTPases in polarized secretory vesicle trafficking.

Esculetin promotes type I procollagen expression in human dermal fibroblasts through MAPK and PI3K/Akt pathways.

Type I collagen is the major constituent of the skin and the reduction of dermal type I collagen content is closely associated with the intrinsic skin aging. We here found that esculetin, 6,7-dihydroxycoumarin, strongly induces type I procollagen expression in human dermal fibroblasts. Esculetin not only increased protein levels of type I procollagen but also increased mRNA levels of COL1A1 but not COL1A2. Esculetin activated the MAPKs (ERK1/2, p38, JNK) and PI3K/Akt pathways, through which it promoted the type I procollagen expression. We also demonstrated that the binding motifs for transcription factor Sp1 occur with the highest frequency in the COL1A1 promoter and that esculetin increases the Sp1 expression through the MAPK and PI3K/Akt pathways. These results suggest that esculetin promotes type I procollagen expression through the MAPK and PI3K/Akt pathways and that Sp1 might be involved in the esculetin-induced type I procollagen expression via activation of the COL1A1 transcription.

Cyclooxygenase-2 induces neoplastic transformation by inhibiting p53-dependent oncogene-induced senescence.

Much in vivo evidence indicates that cyclooxygenase-2 (COX-2) is deeply involved in tumorigenesis. Although it has been proposed that COX-2-derived pro-inflammatory prostanoids mediate the tumorigenic activity of COX-2, the tumorigenic mechanisms of COX-2 are not yet fully understood. Here, we investigated the mechanism by which COX-2 causes transformation from normal cells to malignant cells by using normal murine or human cells. We found that COX-2 inhibits the pro-senescent function of p53 under oncogenic RAS activation, by which it prevents oncogene-induced senescence (OIS) and induces neoplastic transformation. We also found that COX-2 physically interacts with p53 in the nucleus under oncogenic RAS activation, and that this COX-2-p53 interaction rather than the catalytic activity is involved in the COX-2-mediated inhibition of the pro-senescent function of p53 and OIS, and induction of neoplastic transformation. These findings strongly suggest that the oncogenic property of COX-2 is closely related to its ability to inactivate p53 under strong mitogenic signals, and that aberrant activation of the COX-2/a mitogenic oncogene combination can be a potent driving force for tumorigenesis. This study might contribute to our understanding of the molecular basis for the tumorigenic activity of COX-2 and the development of novel anti-tumor drugs targeting COX-2-p53 interactions.

Rapamycin Promotes ROS-Mediated Cell Death via Functional Inhibition of xCT Expression in Melanoma Under γ-Irradiation.

Although many cancer patients are administered radiotherapy for their treatment, the interaction between tumor cells and macrophages in the tumor microenvironment attenuates the curative effects of radiotherapy. The enhanced activation of mTOR signaling in the tumors promotes tumor radioresistance. In this study, the effects of rapamycin on the interaction between tumor cells and macrophages were investigated. Rapamycin and 3BDO were used to regulate the mTOR pathway. In vitro, tumor cells cocultured with macrophages in the presence of each drug under normoxic or hypoxic conditions were irradiated with γ-rays. In vivo, mice were irradiated with γ-radiation after injection with DMSO, rapamycin and 3BDO into tumoral regions. Rapamycin reduced the secretion of IL-4 in tumor cells as well as YM1 in macrophages. Mouse recombinant YM1 decreased the enhanced level of ROS and the colocalized proportion of both xCT and EEA1 in irradiated tumor cells. Human recombinant YKL39 also induced results similar to those of YM1. Moreover, the colocalized proportion of both xCT and LC3 in tumor tissues was elevated by the injection of rapamycin into tumoral regions. Overall, the suppression of mTOR signaling in the tumor microenvironment might be useful for the improvement of tumor radioresistance.

Disruption of nucleocytoplasmic trafficking as a cellular senescence driver.

Senescent cells exhibit a reduced response to intrinsic and extrinsic stimuli. This diminished reaction may be explained by the disrupted transmission of nuclear signals. However, this hypothesis requires more evidence before it can be accepted as a mechanism of cellular senescence. A proteomic analysis of the cytoplasmic and nuclear fractions obtained from young and senescent cells revealed disruption of nucleocytoplasmic trafficking (NCT) as an essential feature of replicative senescence (RS) at the global level. Blocking NCT either chemically or genetically induced the acquisition of an RS-like senescence phenotype, named nuclear barrier-induced senescence (NBIS). A transcriptome analysis revealed that, among various types of cellular senescence, NBIS exhibited a gene expression pattern most similar to that of RS. Core proteomic and transcriptomic patterns common to both RS and NBIS included upregulation of the endocytosis-lysosome network and downregulation of NCT in senescent cells, patterns also observed in an aging yeast model. These results imply coordinated aging-dependent reduction in the transmission of extrinsic signals to the nucleus and in the nucleus-to-cytoplasm supply of proteins/RNAs. We further showed that the aging-associated decrease in Sp1 transcription factor expression was critical for the downregulation of NCT. Our results suggest that NBIS is a modality of cellular senescence that may represent the nature of physiological aging in eukaryotes.

Cyclooxygenase-2 functionally inactivates p53 through a physical interaction with p53.

Cyclooxygenase-2 (COX-2), an endoplasmic reticulum-resident protein, has been known to promote tumorigenesis, but the exact mechanisms involved have not been identified. We have previously reported that COX-2 physically interacts with the tumor suppressor p53 and regulates its function. However, it remains to be elucidated how COX-2 can interact with p53 residing in different compartments and whether their interaction is involved in the regulation of p53 function. We here demonstrated that upon genotoxic stress, COX-2 and p53 accumulate in the nucleus, where they physically interact with one another. We also showed that an amino-terminal region (amino acids 1-126) of COX-2 interacts with the DNA-binding domain of p53. The p53-interacting region was critical for COX-2-mediated inhibition of p53 DNA-binding and transcriptional activity as well as p53- and genotoxic stress-induced apoptosis. In addition, an active site mutant of COX-2 (S516Q) as well as wild-type COX-2 potently inhibited p53 transcriptional activity and genotoxic stress-induced apoptosis. These results suggest that COX-2 principally inhibits p53 function through a catalytic activity-independent mechanism and that COX-2 inhibits p53 function through a physical interaction with p53 in the nucleus. These findings provide novel insight into the action mechanisms of COX-2 and strongly suggest that the functional inactivation of p53 by COX-2 can be one of the mechanisms by which COX-2 promotes tumorigenesis.

Evaluation of various PCR assays for the detection of emetic toxin producing Bacillus cereus.

Because conventional methods for detecting emetic-toxin-producing B. cereus are laborious and costly, various PCR assays, which are easy and cheap, have recently been reported. Therefore, this study estimated and compared the ability of various PCR assays to detect emetic-toxin-producing B. cereus strains isolated in Korea. The PCR assays were performed on 160 B. cereus strains, including 40 emetic-toxin-producing strains. Although the species-specific PCR assays were all shown to be highly specific, the sensitivities varied greatly. The accuracies of the primers were 97.5% (CER), 95.6% (EM1), 96.3% (RE234), 89.4% (CES), and 83.1% (Ces3R/CESR2). Moreover, the CER primer had a higher sensitivity (100%) than all the other primers tested, and a specificity of 96.7%. Thus, the CER primer was shown to be the most effective for screening the emetic-toxin-producing B. cereus strains tested in this study. However, the ability of these PCR assays to identify emetic-toxin-producing B. cereus should also be confirmed using other methods.

DNAJB9 Inhibits p53-Dependent Oncogene-Induced Senescence and Induces Cell Transformation.

DNAJB9 is known to be a member of the molecular chaperone gene family, whose cellular function has not yet been fully characterized. Here, we investigated the cellular function of DNAJB9 under strong mitogenic signals. We found that DNAJB9 inhibits p53-dependent oncogene-induced senescence (OIS) and induces neoplastic transformation under oncogenic RAS activation in mouse primary fibroblasts. In addition, we observed that DNAJB9 interacts physically with p53 under oncogenic RAS activation and that the p53-interacting region of DNAJB9 is critical for the inhibition of p53-dependent OIS and induction of neoplastic transformation by DNAJB9. These results suggest that DNAJB9 induces cell transformation under strong mitogenic signals, which is attributable to the inhibition of p53-dependent OIS by physical interactions with p53. This study might contribute to our understanding of the cellular function of DNAJB9 and the molecular basis of cell transformation.

Discovery of a new primer set for detection and quantification of Ilyonectria mors-panacis in soils for ginseng cultivation.

BACKGROUND: Korean ginseng is an important cash crop in Asian countries. However, plant yield is reduced by pathogens. Among the Ilyonectria radicicola-species complex, I. mors-panacis is responsible for root-rot and replant failure of ginseng in Asia. The development of new methods to reveal the existence of the pathogen before cultivation is started is essential. Therefore, a quantitative real-time polymerase chain reaction method was developed to detect and quantify the pathogen in ginseng soils. METHODS: In this study, a species-specific histone H3 primer set was developed for the quantification of I. mors-panacis. The primer set was used on DNA from other microbes to evaluate its sensitivity and selectivity for I. mors-panacis DNA. Sterilized soil samples artificially infected with the pathogen at different concentrations were used to evaluate the ability of the primer set to detect the pathogen population in the soil DNA. Finally, the pathogen was quantified in many natural soil samples. RESULTS: The designed primer set was found to be sensitive and selective for I. mors-panacis DNA. In artificially infected sterilized soil samples, using quantitative real-time polymerase chain reaction the estimated amount of template was positively correlated with the pathogen concentration in soil samples (R 2  = 0.95), disease severity index (R 2  = 0.99), and colony-forming units (R 2  = 0.87). In natural soils, the pathogen was recorded in most fields producing bad yields at a range of 5.82 ± 2.35 pg/g to 892.34 ± 103.70 pg/g of soil. CONCLUSION: According to these results, the proposed primer set is applicable for estimating soil quality before ginseng cultivation. This will contribute to disease management and crop protection in the future.

Predictive model of Staphylococcus aureus growth on egg products.

Egg products are widely consumed in Korea and continue to be associated with risks of Staphylococcus aureus-induced food poisoning. This prompted the development of predictive mathematical models to understand growth kinetics of S. aureus in egg products in order to improve the production of domestic food items. Egg products were inoculated with S. aureus and observe S. aureus growth. The growth kinetics of S. aureus was used to calculate lag-phase duration (LPD) and maximum specific growth rate (µmax) using Baranyi model as the primary growth model. The secondary models provided predicted values for the temperature changes and were created using the polynomial equation for LPD and a square root model for µmax. In addition, root mean square errors (RMSE) were analyzed to evaluate the suitability of the mathematical models. The developed models demonstrated 0.16-0.27 RMSE, suggesting that models properly represented the actual growth of S. aureus in egg products.

Selective COX-2 inhibitors modulate cellular senescence in human dermal fibroblasts in a catalytic activity-independent manner.

It has been recently proposed that pro-inflammatory genes such as cyclooxygenase-2 (COX-2) play a key role in the aging process. However, it remains unclear whether the pro-inflammatory activity of COX-2 is involved in the aging process and whether COX-2 inhibitors prevent aging. We therefore examined the effect of COX-2 inhibitors on aging in the cellular senescence model of human dermal fibroblasts (HDFs). While the catalytic activity of COX-2 was observed to increase in the senescence process, we found that among three selective COX-2 inhibitors studied, only NS-398 inhibited the senescence whereas celecoxib and nimesulide accelerated the senescence. Non-selective COX inhibitors including aspirin, ibuprofen and flurbiprofen accelerated the senescence. The senescence-regulating effect of selective COX-2 inhibitors had no correlation with cellular reactive oxygen species levels, NF-kappaB activities or protein levels of p53 and p21. We instead found that selective COX-2 inhibitors regulate caveolin-1 expression at transcriptional levels, which was closely associated with the inhibitors' effect on the senescence. Collectively, these results suggest that COX-2 catalytic activity does not mediate HDF senescence and that selective COX-2 inhibitors modulate HDF senescence by a catalytic activity-independent mechanism.

Tumor-secreted factors induce IL-1ß maturation via the glucose-mediated synergistic axis of mTOR and NF-κB pathways in mouse macrophages.

Macrophages are one of the major cell types that produce IL-1ß. IL-1ß maturation occurs via inflammasome activation, and mature IL-1ß is then released from the cell. Secreted IL-1ß mediates inflammatory reactions in various pathological environments, such as those in infectious, autoimmune, and cancerous diseases. Although the mechanism of IL-1ß production has been discovered in infectious and autoimmune diseases, its production mechanism in the tumor microenvironment is unclear. Therefore, the mechanism of IL-1ß production in macrophages in the tumor microenvironment was investigated in this study. First, bone marrow-derived macrophages obtained from C57BL/6 mice were treated with B16F10 tumor-conditioned media (TCM) in vitro. TCM increased the levels of IL-1ß via glucose-mediated activation of the inflammasome. Moreover, TCM enhanced the activation of both NF-κB and mTOR pathways in a glucose-dependent manner. In particular, the expression levels of mTORC1 component proteins were dependent on the TCM-induced activation of NF-κB signaling. In addition, TCM affected ASC-ASC interactions through increasing intracellular reactive oxygen species levels. Finally, glucose inhibition by inoculation with 2-deoxy-D-glucose in vivo decreased the IL-1ß levels in both the blood and tumor region of B16F10-bearing C57BL/6 mice relative to those in PBS-injected tumor-bearing mice. These results suggest that glucose supplied from blood vessels might be important for IL-1ß production in tumor-associated macrophages via the integrated signals of the NF-κB and mTOR pathways in the tumor microenvironment.