M. smegmatis response to energy- and oxygen-limitation in continuous culture
ABSTRACT: Transcriptional profiling of M. smegmatis grown at 69h doubling time compared to 4.6h doubling time both at 50% air saturation. Transcriptional profiling of M. smegmatis grown at 69h doubling time with 50%, 2.5% and 0.6% air saturation. Two-condition experiment. Biological replicates: 5 independently grown and harvested. One replicate per array.
Mycobacteria are a group of obligate aerobes that require oxygen for growth, but paradoxically have the ability to survive and metabolize under hypoxia. The mechanisms responsible for this metabolic plasticity are unknown. Here, we report on the adaptation of Mycobacterium smegmatis to slow growth rate and hypoxia using carbon-limited continuous culture. When M. smegmatis is switched from a 4.6 h to a 69 h doubling time at a constant oxygen saturation of 50%, the cells respond through the down r ...[more]
Project description:Transcriptional profiling of M. smegmatis MB100pruR vs. MB100 (isogenic parent) grown in serumvials on Hartmans de Bont medium supplemented with glycerol and proline Two-condition experiment. Biological replicates: 4 independently grown and harvested. One replicate per array.
Project description:Transcriptional profiling of M. smegmatis mc2155 grown on Hartmans de Bont (HdB) supplemented with 0.2% glycerol and 0.05% Tween80 challenged with 2 μg/ml Bedaquiline and Dimethyl sulfoxide (DMSO) Two-condition experiment. Biological replicates: 5 independently grown and harvested. One replicate per array.
Project description:To identify the AmtR regulon of Mycobacterium smegmatis, we created a markerless deletion of the amtR gene in the background of strain M. smegmatis mc2155 (wild-type) and compared the transcription profile of both strains grown in batch culture under aerobic conditions on Hartmans de Bont medium supplemented with glycerol (carbon source) and lysine (sole nitrogen source) using microarray. Cells were harvested in early exponential growth stage.
Project description:DosR is the regulator of a two-component system in mycobacteria that senses oxygen concentration and the redox state of the cells. To determine the DosR regulon, the transcriptomes of M. smegmatis mc2155 and the ΔdosR cells were compared by microarray at 10 hours following induction of oxygen-limitation in serum vials. 4 biological replicates incl. 2 dye swaps. 3 technical replicates per array
Project description:Comparing transciptional profile of a M. smegmatis mc2155 ΔsigF strain and wild type (control) in in vitro culture at two time points (exponential phase and stationary phase) for identification of SigF-dependent genes. Analysis of 2 time points: exponential and stationary phase. 4 biological replicates comparing expression of wild type (control) and ΔsigF strain incl. dye swaps for each time point. 3 technical replicates per array
Project description:Transcriptional profiling of M. smegmatis JR121 expressing VapC and VapBC grown in flasks on Hartmans de Bont medium supplemented with 0.2% glycerol Comparing transcriptional response of strain JR121 to conditional expression of VapC toxin compared with the expression of VapBC complex. Biological replicates: 4 independently grown and harvested. One replicate per array.
Project description:Transcriptional profiling of M. smegmatis and Dcrp1 grown in flasks on Hartmans de Bont medium supplemented with 10 mM glycerol. Transcriptional profiling of M.smegmatis HLA102 harboring tetracycline inducible vector pMind containing the Crp2 and M. smegmatis harboring pMind grown in flasks on Hartmans de Bont medium supplemented with 10 mM glycerol Comparing transcriptional response of wild-type compared with the deletion of crp1 gene (Msmeg_0539). Biological replicates: 4 independently grown and harvested. One replicate per array. Comparing transcriptional response of strain HLA102 to conditional expression of Crp2 (Msmeg_6189) compared with the wild-type with empty vector pMind. Biological replicates: 4 independently grown and harvested. One replicate per array.
Project description:The transcription factor complex AP-1 (Activator protein 1) is composed of Jun (c-Jun, JunB, JunD) and Fos proteins (c-Fos, FosB, Fra-1, Fra-2) which control a variety of stress responses, including cell proliferation, apoptosis, inflammation, wound healing, and cancer. Individual Fos proteins have been thoroughly studied in gain- and loss-of-function mouse models, which revealed important functions in bone cell proliferation and differentiation. We have recently demonstrated that loss of Fra-2 causes perinatal lethality and severe osteopenia due to several cellular defects, including a chondrocyte differentiation defect and a control of osteoclast survival and size. Moreover, we have reported a profibrogenic function of Fra-2 in transgenic mice, in which ectopic expression of Fra-2 in various organs resulted in generalized fibrosis with predominant manifestations in the lung. Fra-2 knock-out newborns have increased numbers and size of osteoclasts in vivo. The pulmonary phenotype observed in Fra-2Tg mice is characterized by vascular remodeling and obliteration of pulmonary arteries, which coincides with expression of osteopontin, an AP-1 target gene involved in vascular remodeling and fibrogenesis. These alterations are followed by inflammation; release of profibrogenic factors, such as IL-4, insulin-like growth factor 1, and CXCL5. The expression profiling study was performed to analyse changes in transcript levels in lung over a period of time. Total RNA of four mutant male animals at each time point (age: 6, 10 and 14 weeks) were hybridised versus a pool of total RNA of four wild type mice of the corresponding age. For each mutant animal, two technical chip hybridisations were performed, including a dye-swap experiment (in total, 8 hybridisation of each time point = 2 technical replicates x 4 biological replicates).
Project description:The molecular mechanisms underlying the development and progression of sugarcane mosaic virus (SCMV) infection in maize are poorly understood. A transcript profiling study based on maize unigene-microarrays was conducted to identify genes associated with SCMV resistance in the near isogenic line (NIL) pair F7+ (SCMV resistant) and F7 (susceptible). Four comparisons were conducted, which is addressing constitutive genetic discrepancy (Non-infected F7 vs. Non-infected F7+), inducible genetic discrepancy (Infected F7 vs. Infected F7+), compatible reaction (Non-infected F7 vs. Infected F7), and incompatible reaction (Non-infected F7+ vs. Infected F7+).
Project description:The type III effector (T3E) AWR5 from the phytopathogen Ralstonia solanacearum causes disease in many plants relevant in agriculture. Heterologous expression in yeast of AWR5 from an integrated tetO promoter caused strong growth inhibition. In this series of experiments we investigate the possible changes in the transcriptional profile in a time-course (2, 4 and 6 h) response to AWR5 production. Yeast strains were grown overnight in rich YPD medium with doxycycline 15 µg/ml (repressing conditions), then normalized to OD600=0.05 and grown resumed in YPD+dox (non-inducing conditions) or YPD (inducing conditions). Samples were taken at 2, 4 or 6 hours for each condition. Two biological replicates were made for each time point.