Dataset Information

Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses.

ABSTRACT: Constraint-based approaches have been used for integrating data in large-scale metabolic networks to obtain insights into metabolism of various organisms. Due to the underlying steady-state assumption, these approaches are usually not suited for making predictions about metabolite levels. Here, we ask whether we can make inferences about the variability of metabolite levels from a constraint-based analysis based on the integration of transcriptomics data. To this end, we analyze time-resolved transcriptomics and metabolomics data from Arabidopsis thaliana under a set of eight different light and temperature conditions. In a previous study, the gene expression data have already been integrated in a genome-scale metabolic network to predict pathways, termed modulators and sustainers, which are differentially regulated with respect to a biochemically meaningful data-driven null model. Here, we present a follow-up analysis which bridges the gap between flux- and metabolite-centric methods. One of our main findings demonstrates that under certain environmental conditions, the levels of metabolites acting as substrates in modulators or sustainers show significantly lower temporal variations with respect to the remaining measured metabolites. This observation is discussed within the context of a systems-view of plasticity and robustness of metabolite contents and pathway fluxes. Our study paves the way for investigating the existence of similar principles in other species for which both genome-scale networks and high-throughput metabolomics data of high quality are becoming increasingly available.

SUBMITTER: Topfer N

PROVIDER: S-EPMC4063599 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

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Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses.

Töpfer Nadine N Scossa Federico F Fernie Alisdair A Nikoloski Zoran Z

PLoS computational biology 20140619 6

Constraint-based approaches have been used for integrating data in large-scale metabolic networks to obtain insights into metabolism of various organisms. Due to the underlying steady-state assumption, these approaches are usually not suited for making predictions about metabolite levels. Here, we ask whether we can make inferences about the variability of metabolite levels from a constraint-based analysis based on the integration of transcriptomics data. To this end, we analyze time-resolved tr ...[more]

PMID: 24946036

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Project description:In response to cold or diet, fatty acids are dissipated into heat through uncoupling protein 1 (UCP1) in brown adipose tissue (BAT). This process is termed non-shivering thermogenesis, which is important for body temperature maintenance and contributes to obesity pathogenesis. Thermogenic enhancement has been considered a promising anti-obesity strategy. Ghrelin and its receptor Growth Hormone Secretagogue Receptor (GHS-R) have critical roles in energy intake, nutrient sensing, and lipid metabolism. We previously reported that global Ghsr-knockout mice have increased energy expenditure due to enhanced thermogenesis. To determine the site of action for GHS-R mediated thermogenesis, we generated brown adipocyte-specific Ghsr knockout mice (UCP1-CreER/Ghsrf/f) and assessed thermogenic responses under regular diet (RD) fed homeostatic metabolic state or high-fat diet (HFD) fed metabolically-impaired obese state, under normal or cold housing environment. Under a RD-feeding, UCP1-CreER/Ghsrf/f mice showed increased body fat and a slightly elevated core body temperature under cold but not under normal temperature. Consistently, the expression of thermogenic genes in BAT of RD-fed UCP1-CreER/Ghsrf/f mice was increased in reposes to cold. Under HFD feeding, HFD-fed UCP1-CreER/Ghsrf/f mice showed no difference in body fat or body temperature under either normal or cold exposure. Interestingly, the expression of thermogenic genes in BAT of HFD-fed UCP1-CreER/Ghsrf/f mice was upregulated under normal temperature but downregulated under cold exposure. Overall, our data show that GHS-R has cell-autonomous effect in brown adipocytes, and GHS-R regulates BAT thermogenic activity in a temperature- and metabolic state-dependent manner. The thermogenic effect of GHS-R in BAT is more pronounced in cold environment and differentially variable based on metabolic state; under cold exposure, GHS-R inhibition in BAT activates thermogenesis under homeostatic state but suppresses thermogenesis under obese state. Our finding collectively suggests that GHS-R in BAT, acting as a "metabolic thermostat", differentially regulates thermogenesis in response to different metabolic and thermal stimuli.

Project description:BACKGROUND: The completion of whole-genome sequencing for Corynebacterium pseudotuberculosis strain 1002 has contributed to major advances in research aimed at understanding the biology of this microorganism. This bacterium causes significant loss to goat and sheep farmers because it is the causal agent of the infectious disease caseous lymphadenitis, which may lead to outcomes ranging from skin injury to animal death. In the current study, we simulated the conditions experienced by the bacteria during host infection. By sequencing transcripts using the SOLiDTM 3 Plus platform, we identified new targets expected to potentiate the survival and replication of the pathogen in adverse environments. These results may also identify possible candidates useful for the development of vaccines, diagnostic kits or therapies aimed at the reduction of losses in agribusiness. RESULTS: Under the 3 simulated conditions (acid, osmotic and thermal shock stresses), 474 differentially expressed genes exhibiting at least a 2-fold change in expression levels were identified. Important genes to the infection process were induced, such as those involved in virulence, defence against oxidative stress, adhesion and regulation, and many genes encoded hypothetical proteins, indicating that further investigation of the bacterium is necessary. The data will contribute to a better understanding of the biology of C. pseudotuberculosis and to studies investigating strategies to control the disease. CONCLUSIONS: Despite the veterinary importance of C. pseudotuberculosis, the bacterium is poorly characterised; therefore, effective treatments for caseous lymphadenitis have been difficult to establish. Through the use of RNAseq, these results provide a better biological understanding of this bacterium, shed light on the most likely survival mechanisms used by this microorganism in adverse environments and identify candidates that may help reduce or even eradicate the problems caused by this disease.

Dataset Information

Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses.

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Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses.

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