A Genetic Selection for Mycobacterium smegmatis Mutants Tolerant to Killing by Sodium Citrate Defines a Combined Role for Magnesium Homeostasis and Osmotic Stress in Cell Death
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ABSTRACT:
PROVIDER: PRJNA749248 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15224025_1.fastq.gz | Fastqsanger.gz | |||
| SRR15224025_2.fastq.gz | Fastqsanger.gz | |||
| SRR15224026_1.fastq.gz | Fastqsanger.gz | |||
| SRR15224026_2.fastq.gz | Fastqsanger.gz | |||
| SRR15224027_1.fastq.gz | Fastqsanger.gz |
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Project description:Regulation of Mycobacterium smegmatis gene expression by treatment with sodium citrate.
2023-09-06 | GSE180696 | GEO
Project description:Adequate bowel cleansing is important for a completeness of colonoscopy and detection of colon polyps. Inadequate bowel preparation leads to longer duration of colonoscopy and obscured mucosal visualization resulting in missed lesions.
Bowel cleansing agents are simply classified into the large volume, iso-osmotic polyethylene glycol (PEG) based solutions or the small volume osmotically active agents, such as sodium picosulphate with magnesium citrate (SPMC).
There are rare reports that compare directly conventional polyethylene glycol (PEG) solution and sodium picosulphate with magnesium citrate (SPMC) for bowel preparation in korea.
The aim of this study is to compare the efficacy, safety, and tolerability of different regimens of SPMC and PEG solution.
| 2139045 | ecrin-mdr-crc
Project description:To compare the polyp and adenoma detection rate of MOVIPREP versus an oral Sodium Picosulfate/Magnesium Citrate solution.
| 2132271 | ecrin-mdr-crc
Project description:Mycobacterium smegmatis is a model non-pathogenic mycobacterium that is efficiently killed by macrophages. Here, we explore the role of NF-?B in the innate immune response, focusing in detail on the mechanisms of the first killing period (1-4h) of M. smegmatis which coincides with phagosome-lysosome fusion. We show that infection of macrophages with M. smegmatis induces an activation of NF-?B and this activation is required for killing since treatment of macrophages with NF-?B inhibitors or siRNA silencing of the NF-?B subunit p65 increases bacterial survival. NF-?B induced proteins were thus hypothesized to be essential during the first phase of M. smegmatis killing. We therefore identified, using RNA microarray, the genes that were regulated during infection in the absence and presence of NF-?B inhibitors. By subtraction this provided a list of pro-inflammatory proteins that were under the control of NF-?B and putatively involved in the killing response. Among these category of genes were those for lysosomal enzymes and membrane trafficking regulators, including Cathepsins, LAMP-2 and Rab34, are regulated by NF-?B. Moreover, inhibition of NF-?B signaling retarded the delivery of v-ATPase, LAMP-2, CtsZ and CtsH thereby impairing the maturation of mycobacterial phagosomes. Collectively; our data provide the first compelling evidence that the innate immune response via NF-?B activation is linked to phagosome fusion with lysosomes that is essential for killing of mycobacteria. Keywords: NFkB inhibitor treated vs untreated The study includes J774 macrophage cell lines which are infected with Mycobacterium smegmatis in the presence and absense of NFkB inhibitor SC-514.Total RNA was isolated from individual samples and each sample was hybridised to CodeLink Mouse whole genome bioarray slides.This study was intended to know the role of NFkB regulated genes in killing non-pathogenic mycobacteria during 4 hour post infection of macrophages.
2007-10-23 | E-GEOD-8999 | biostudies-arrayexpress
Project description:Mycobacteria can colonize environments where the availability of metal ions is limited. Biological or inorganic chelators play an important role in limiting metal availability, and we developed a model to examine Mycobacterium smegmatis survival in the presence of the chelator sodium citrate. We observed that instead of restricting M. smegmatis growth, concentrated sodium citrate killed M. smegmatis. RNAseq analysis during sodium citrate treatment revealed transcriptional signatures of metal starvation and hyperosmotic stress. Notably, metal starvation and hyperosmotic stress, individually, do not kill M. smegmatis under these conditions. A forward genetic transposon selection was conducted to examine why sodium citrate was lethal, and several sodium-citrate-tolerant mutants were isolated. Based on the identity of three tolerant mutants, mgtE, treZ, and fadD6, we propose a dual stress model of killing by sodium citrate, where sodium citrate chelate metals from the cell envelope and then osmotic stress in combination with a weakened cell envelope causes cell lysis. This sodium citrate tolerance screen identified mutants in several other genes with no known function, with most conserved in the pathogen M. tuberculosis. Therefore, this model will serve as a basis to define their functions, potentially in maintaining cell wall integrity, cation homeostasis, or osmotolerance. IMPORTANCE Bacteria require mechanisms to adapt to environments with differing metal availability. When Mycobacterium smegmatis is treated with high concentrations of the metal chelator sodium citrate, the bacteria are killed. To define the mechanisms underlying killing by sodium citrate, we conducted a genetic selection and observed tolerance to killing in mutants of the mgtE magnesium transporter. Further characterization studies support a model where killing by sodium citrate is driven by a weakened cell wall and osmotic stress, that in combination cause cell lysis.
| S-EPMC10597346 | biostudies-literature
Project description:Mycobacterium smegmatis is a model non-pathogenic mycobacterium that is efficiently killed by macrophages. Here, we explore the role of NF-κB in the innate immune response, focusing in detail on the mechanisms of the first killing period (1-4h) of M. smegmatis which coincides with phagosome-lysosome fusion. We show that infection of macrophages with M. smegmatis induces an activation of NF-κB and this activation is required for killing since treatment of macrophages with NF-κB inhibitors or siRNA silencing of the NF-κB subunit p65 increases bacterial survival. NF-κB induced proteins were thus hypothesized to be essential during the first phase of M. smegmatis killing. We therefore identified, using RNA microarray, the genes that were regulated during infection in the absence and presence of NF-κB inhibitors. By subtraction this provided a list of pro-inflammatory proteins that were under the control of NF-κB and putatively involved in the killing response. Among these category of genes were those for lysosomal enzymes and membrane trafficking regulators, including Cathepsins, LAMP-2 and Rab34, are regulated by NF-κB. Moreover, inhibition of NF-κB signaling retarded the delivery of v-ATPase, LAMP-2, CtsZ and CtsH thereby impairing the maturation of mycobacterial phagosomes. Collectively; our data provide the first compelling evidence that the innate immune response via NF-κB activation is linked to phagosome fusion with lysosomes that is essential for killing of mycobacteria. Keywords: NFkB inhibitor treated vs untreated
2007-10-23 | GSE8999 | GEO
Project description:RNA-seq of Mycobacteriophage Island3 infection of Mycolicibacterium smegmatis mc2155, Mycolicibacterium smegmatis mc2155(Butters), and Mycolicibacterium smegmatis mc2155(Buttersgp57r) to assess the impact of Butters lysogen and specifically Buttersgp57r on transcript levels of island3 during infection.
2022-12-24 | GSE221406 | GEO
Project description:Mouse macrophages J774A.1 were pre-treated with the anti-inflammatory lipid eicosapenaenoic acid (EPA) or the pro-inflammatory lipid ceramide (Cer) for 3h. Macrophages were then infected with Mycobacterium smegmatis for 1h, and total RNA was collected. In a parallel experiment, infected macrophages were infected for 1h, 4h and 24h. At these time points, macrophages were lysed, bacteria was collected and quantified by the Colony Forming Units (CFU) Assay. This provided the kinetics of the killing of Mycobacteria inside mouse macrophages. CFU experiments revealed that cells pre-treated with EPA showed an increased number of bacteria inside macrophages, in contrast to cells pre-treated with Cer. To dissect the molecular mechanisms involved in the survival and killing of mycobacteria infected macrophages, mediated by lipids, gene expression studies were performed. Cultures of Mycobacterium smegmatis mc2155 harbouring a p19-(long lived) EGFP plasmid were grown to exponential growth phase. Bacteria were pelleted, washed in PBS and resuspended in medium DMEM with a multiplicity of infection (MOI) of 10 (10 bacteria per macrophage). Clumps of bacteria were removed by ultrasonic treatment of bacterial suspensions in an ultrasonic water bath for 15 minutes, followed by a low speed centrifugation for 2 minutes. Mouse macrophages J774A.1 were pre-.treated with the anti-inflammatory lipid eicosapenaenoic acid (EPA) or the pro-inflammatory lipid ceramide (Cer), 3h before infection. Mouse macrophages J774A.1 were infected with Mycobacterium smegmatis mc2155 for 1h, at 37M-BM-:C and 5% CO2. After 1h of infection, cells were washed with PBS. After washing, 1 ml Trizol was added per well, to collect total RNA. The experimental condition were: samples 1.1, 1.2, 1.3: Untreated macrophages; samples 2.1, 2.2, 2.3: Mock treated macrophages (ethanol 1ul/ml); samples 3.1, 3.2, 3.3: EPA (15uM) treated macrophages (ethanol 1ul/ml); samples 4.1, 4.2, 4.3: Cer (5ug/ml) treated macrophages (ethanol 1ul/ml); samples 5.1, 5.2, 5.3: Untreated macrophages, infected with Mycobacterium smegmatis mc2155 for 1h; samples 6.1, 6.2, 6.3: Mock treated macrophages (ethanol 1ul/ml) infected with Mycobacterium smegmatis mc2155 for 1h; samples 7.1, 7.2, 7.3: EPA (15uM) treated macrophages (ethanol 1ul/ml) infected with Mycobacterium smegmatis mc2155 for 1h; samples 8.1, 8.2, 8.3: Cer (5ug/ml) treated macrophages (ethanol 1ul/ml) infected with Mycobacterium smegmatis mc2155 for 1h; In a parallel experiment, infected macrophages remained with the bacteria for 1h, 4h and 24h after infection. After these time points, the macrophages were lysed, the bacteria was collected and quantified by the Colony Forming Units (CFU) Assay. This provided the kinetics of the killing of non-pathogenic intracellular bacteria inside mouse macrophages. For the CFU assay, after 1h of infection, cells were washed with PBS and Gentamicin (10ug/ml) in DMEM to kill the extracellular bacteria. At discrete time points, cells were washed with PBS and lysed with sterilized water. Quantitative cultures of bacteria were performed in a 10-fold serial dilutions, inoculated on 7H10 agar plates. 5ul were plated in triplicate and the number of colonies were counted after 48h.
2015-01-20 | E-GEOD-27277 | biostudies-arrayexpress
Project description:Background and study aimsPolyethylene glycol-based electrolyte solutions (PEG-ELS) and the combination of sodium picosulfate/magnesium citrate (SPMC) are commonly used bowel preparation agents. The aim of the present study was to compare the two agents with regard to cleansing efficacy and tolerance among individuals scheduled for outpatient colonoscopy.Materials and methodsThe 368 colonoscopy outpatients at three Norwegian hospitals were randomized to bowel lavage with either PEG-ELS or SPMC. Compliance and patient tolerance were evaluated using a patient questionnaire. Bowel cleansing was evaluated using the Ottawa Bowel Preparation Quality Scale (OBPS), a validated scoring system with scores between 0 (best) and 14.ResultsThere was no difference in the cleansing quality between the PEG-ELS and SPMC groups (median OBPS 5.0 in both groups). The group that received SPMC reported better overall patient tolerance than the PEG-ELS group (72.6 % vs 59.0 % reporting no or slight discomfort, P < 0.01). Compliance with the recommended total fluid intake (4 L) was better in the SPMC group than in the PEG-ELS group (94.2 % vs 81.2 % respectively, P < 0.01); moreover, the polyp detection rate was superior (34.3 % vs 23.3 %, P = 0.02).ConclusionPEG-ELS and SPMC are equally effective in cleansing efficacy, but SPMC was better tolerated by patients and resulted in superior patient compliance and polyp detection rate.Clinical trial registrationNCT01624454.
| S-EPMC4423298 | biostudies-literature
Project description:Mycobacterium smegmatis SigF is a group III sigma factor. Its ortholog in M. tuberculosis is reported to have role in regulation and function of cell wall components. In present study we have created an M. smegmatis ΔsigF mutant by allele exchange method. M. smegmatis sigF mutant shows non pigmented phenotype and is more sensitive to hydrogen peroxide generated oxidative stress. DNA microarray analysis of M. smegmatis wild type and ΔsigF mutant suggests that SigF in this species controls the expression of several energy and central intermediary metabolism genes along with regulation of carotenoid biosynthesis.
2010-08-20 | GSE19774 | GEO