ABSTRACT: GNPS melHKO Mm
untargeted metabolomics
(glycerol/propionate/cholesterol/oleic acid/pyruvate as sole carbon source)
RP C18/HILIC/HIPLEX column
Positive/Negative phase
Project description:RNA-Seq results accompanying submission of a manuscript: "Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis" describing the role of cholesterol and vitamin B12 in shaping the transcriptome of the Mycobacterium tuberculosis H37Rv and M. tuberculosis ∆prpR - propionate regulator (PrpR) mutant. Next generation sequencing results are provided in three independent biological replicates for each strain growing in three different media - minimal medium with glycerol or cholesterol as the sole carbon source and standard 7H9/10% OADC medium. The influence of vitamin B12 on M. tuberculosis transcriptome was analysed on 7H9/10% OADC medium supplemented with B12. The study allowed us to re-establish the list of genes potentially involved in cholesterol metabolism. We further proposed a novel regulatory function of vitamin B12 and PrpR, a propionate regulator, in coordinated cholesterol breakdown metabolite dissipation and virulent phenotype induction. Finally, we demonstrated that a key role of cholesterol in Mtb metabolism is not only providing carbon and energy but also inducing a transcriptome remodeling program that helps in developing tolerance to the unfavorable host cell environment.
Project description:The purpose of this study was to examine how Mtb integrates acidic pH and available carbon sources as environmental cues to regulate its metabolism and growth rate. RNA-seq transcriptional profiling of M. tuberculosis growing at acidic or neutral pH, in pyruvate or glycerol, was examined. These studies identified carbon source-dependent and -independent pH-dependent adaptations.
Project description:The purpose of this study was to examine how Mtb integrates acidic pH and available carbon sources as environmental cues to regulate its metabolism and growth rate. RNA-seq transcriptional profiling of M. tuberculosis growing at acidic or neutral pH, in pyruvate or glycerol, was examined. These studies identified carbon source-dependent and -independent pH-dependent adaptations. Mtb strain CDC1551 was grown in standing T-75 flasks in 40 mL of medium seeded an initial OD of 0.1. We examined medium in four conditions pH 7.0 10 mM glycerol, pH 5.7 10 mM glycerol, pH 7.0 10 mM pyruvate, pH 5.7 10 mM pyruvate. Following 3 days of incubation at 37C, RNA was isolated from the bacterial cultures and used for RNA-seq.
Project description:Rsf1p is a putative transcription factor required for efficient growth using glycerol as sole carbon source but not for growth on the alternative respiratory carbon source ethanol. We use microarrays to determine the differences in the transcriptional program between the Δrsf1 mutant and the wild type during respiratory growth on glycerol as well as the transition to growth on glycerol as sole carbon source. Keywords: Mutant analysis during timecourse following switching carbon source from dextrose to glycerol
Project description:This dataset contains the gene expression signature in triplicates of Escherichia coli BW25113 growing exponentially on eight different environments: minimal medium supplemented with 5 g/L of Glucose, Galactose, Glycerol, Gluconate, Fructose, Pyruvate, Succinate or Acetate as the sole carbon source.
Project description:E. coli isolates from different CF patients demonstrate increased growth rate when grown with glycerol, a major component of fecal fat, as the sole carbon source compared to E. coli from healthy controls. CF and control E. coli isolates have differential gene expression when grown in minimal media with glycerol as the sole carbon source. While CF isolates display a growth promoting transcriptional profile, control isolates engage stress and stationary phase programs, which likely results in slower growth rates.
Project description:Transcriptional profile of wild type L. monocytogenes (EGDe) and a pycA mutant strain was compared on growth in BHI. The human pathogen L. monocytogenes is a facultatively intracellular bacterium that survives and replicates in the cytosol of many mammalian cells. The listerial metabolism, especially under intracellular conditions , is still poorly understood. Recent studies analyzed the carbon metabolism of L. monocytogenes by the 13C-isotopologue perturbation method in a defined minimal medium containing [U-13C6]glucose. It was shown that these bacteria produce oxaloacetate mainly by carboxylation of pyruvate due to an incomplete tricarboxylic acid cycle. Here we report that a pycA insertion mutant defective in pyruvate carboxylase (PYC) still grows, albeit at a reduced rate, in BHI medium, but is unable to multiply in a defined minimal medium with glucose or glycerol 36 as carbon source. Transcriptional profiling was performed on the pycA mutant and the wild type strain grown in BHI to get a closer insight into the effect of the pycA mutation in Listeria monocytogenes.
Project description:Transcriptional profiling of Alcanivorax borkumensis cells, grown on either pyruvate or hexadecane, canola and diesel as carbon source.
Project description:Diatoms are prominent marine microalgae, interesting not only from an ecological point of view, but also for their possible use for biotechnology applications. They can be cultivated in phototrophic conditions, using sunlight as the only energy source. Some diatoms, however, can also grow in mixotrophic mode, where both light and external reduced carbon contribute to biomass accumulation. In this study, we investigated the consequences of mixotrophy on the growth and metabolism of the pennate diatom Phaeodactylum tricornutum, using glycerol as a source of reduced carbon. Transcriptomic, metabolomic and physiological data indicate that glycerol affects the central-carbon, carbon-storage and lipid metabolism of the diatom. In particular, glycerol addition mimics some typical responses of nitrogen limitation on lipid metabolism at the level of TAG accumulation and fatty acid composition. However, this compound does not diminish photosynthetic activity and cell growth, at variance with nutrient limitation, revealing essential aspects of the metabolic flexibility of these microalgae and suggesting possible biotechnological applications of mixotrophy.
Project description:The changes in protein composition of E. coli were studied in a global proteomic approach for aerobic growth without or with fumarate as carbon source (glycerol + O2, fumarate + O2, respectively) and anaerobic growth without or with fumarate as carbon source (glycerol + DMSO, glycerol + DMSO + fumarate, respectively). The experiments should unravel the changes in response to fumarate under aerobic (i) and anaerobic (ii) conditions, and more generally (iii) the fumarate proteome under aerobic versus anaerobic conditions. Fumarate was used as the C4DC due to its capability to support aerobic and anaerobic growth, and glycerol was used as the alternative carbon source that exerts no or only weak carbon catabolite repression.