scholarly journals An integrated computational and experimental study to elucidate Staphylococcus aureus metabolism

2019 ◽  
Author(s):  
Mohammad Mazharul Islam ◽  
Vinai C. Thomas ◽  
Matthew Van Beek ◽  
Jong-Sam Ahn ◽  
Abdulelah A. Alqarzaee ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Environmental Changes ◽  
Model Performance ◽  
Metabolic Model ◽  
Exchange Reactions ◽  
Chemical Balance ◽  
Manual Curation ◽  
Specific Regulation ◽  
Reaction Stoichiometry

AbstractStaphylococcus aureus is a metabolically versatile pathogen that colonizes nearly all organs of the human body. A detailed and comprehensive knowledge of staphylococcal metabolism is essential to understanding its pathogenesis. To this end, we have reconstructed and experimentally validated an updated and enhanced genome-scale metabolic model of S. aureus USA300_FPR3757. The model combined genome annotation data, reaction stoichiometry, and regulation information from biochemical databases and previous strain-specific models. Reactions in the model were checked and fixed to ensure chemical balance and thermodynamic consistency. To further refine the model, growth assessment of 1920 non-essential mutants from the Nebraska Transposon Mutant Library was performed and metabolite excretion profiles of important mutants in carbon and nitrogen metabolism were determined. The growth and no-growth inconsistencies between the model predictions and in vivo essentiality data were resolved using extensive manual curation based on optimization-based reconciliation algorithms. Upon intensive curation and refinements, the model contains 840 metabolic genes, 1442 metabolites, and 1566 reactions including transport and exchange reactions. To improve the accuracy and predictability of the model to environmental changes, condition-specific regulation information curated from the existing knowledgebase was incorporated. These critical additions improved the model performance significantly in capturing gene essentiality, substrate utilization, and metabolite production capabilities and increased the ability to generate model-based discoveries of therapeutic significance. Use of this highly curated model will enhance the functional utility of omics data and, therefore, serve as a resource to support future investigations of S. aureus and to augment staphylococcal research worldwide.

scholarly journals Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition

2020 ◽  
Author(s):  
Christian Schulz ◽  
Tjaša Kumelj ◽  
Emil Karlsen ◽  
Eivind Almaas
Keyword(s):  
Environmental Conditions ◽  
Environmental Changes ◽  
Model Performance ◽  
Optimal Growth ◽  
Metabolic Model ◽  
Biomass Composition ◽  
Phenotypic Traits ◽  
Metabolic Modelling ◽  
Genome Scale

AbstractGenome-scale metabolic modeling is an important tool in understanding metabolism, by enhancing collation of knowledge, interpretation of data, and prediction of metabolic capabilities. A central assumption in the construction and use of genome-scale models is that the in vivo organism is evolved for optimal growth, where growth is represented by flux through a biomass objective function (BOF). While the specific composition of the BOF is crucial, its formulation is often inherited from similar organisms due to the experimental challenges associated with its proper determination.However, a cell’s macro-molecular composition is not fixed and it responds to changes in environmental conditions. As a consequence, initiatives for the high-fidelity determination of cellular biomass composition have been launched. Thus, there is a need for a mathematical and computational framework capable of using multiple measurements of cellular biomass composition in different environments. Here, we propose two different computational approaches for directly addressing this challenge: Biomass Trade-off Weighting (BTW) and Higher-dimensional-plane InterPolation (HIP).In lieu of experimental data on biomass composition-variation in response to changing nutrient environment, we assess the properties of BTW and HIP using three hypothetical, yet biologically plausible, BOFs for the Escherichia coli genome-scale metabolic model iML1515. We find that the BTW and HIP formulations have a significant impact on model performance and phenotypes. Furthermore, the BTW method generates larger growth rates in all environments when compared to HIP. Using acetate secretion and the respiratory quotient as proxies for phenotypic changes, we find marked differences between the methods as HIP generates BOFs more similar to a reference BOF than BTW. We conclude that the presented methods constitute a first conceptual step in developing genome-scale metabolic modelling approaches capable of addressing the inherent dependence of cellular biomass composition on nutrient environments.Author summaryChanges in the environment promote changes in an organism’s metabolism. To achieve balanced growth states for near-optimal function, cells respond through metabolic rearrangements, which may influence the biosynthesis of metabolic precursors for building a cell’s molecular constituents. Therefore, it is necessary to take the dependence of biomass composition on environmental conditions into consideration. While measuring the biomass composition for some environments is possible, and should be done, it cannot be completed for all possible environments.In this work, we propose two main approaches, BTW and HIP, for addressing the challenge of estimating biomass composition in response to environmental changes. We evaluate the phenotypic consequences of BTW and HIP by characterizing their effect on growth, secretion potential, respiratory efficiency, and gene essentiality of a cell.Our work constitutes a first conceptual step in accounting for the influence of growth conditions on biomass composition, and in turn the biomass composition’s effect on metabolic phenotypic traits, within constraint-based modelling. As such, we believe it will improve the relevance of constraint-based methods in metabolic engineering and drug discovery, since the biosynthetic potential of microbes for generating industrially relevant products or drugs often is closely linked to their biomass composition.

scholarly journals Ser/Thr phospho-regulation by PknB and Stp mediates bacterial quiescence and antibiotic persistence in Staphylococcus aureus

2021 ◽  
Author(s):  
Markus Huemer ◽  
Srikanth Mairpady Shambat ◽  
Sandro Pereira ◽  
Lies Van Gestel ◽  
Judith Bergada-Pijuan ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Ribosomal Proteins ◽  
Environmental Changes ◽  
Acid Stress ◽  
Elongation Factor ◽  
Growth Delay ◽  
Lag Phase ◽  
Cellular Processes ◽  
Translational Activity

Staphylococcus aureus colonizes 30 to 50% of healthy adults and can cause a variety of diseases, ranging from superficial to life-threatening invasive infections such as bacteraemia and endocarditis. Often, these infections are chronic and difficult-to-treat despite adequate antibiotic therapy. Most antibiotics act on metabolically active bacteria in order to eradicate them. Thus, bacteria with minimized energy consumption resulting in metabolic quiescence, have increased tolerance to antibiotics. The most energy intensive process in cells - protein synthesis - is attenuated in bacteria entering into quiescence. Eukaryote-like serine/threonine kinases (STKs) and phosphatases (STPs) can fine-tune essential cellular processes, thereby enabling bacteria to quickly respond to environmental changes and to modulate quiescence. Here, we show that deletion of the only annotated functional STP, named Stp, in S. aureus leads to increased bacterial lag-phase and phenotypic heterogeneity under different stress challenges, including acidic pH, intracellular milieu and in vivo abscess environment. This growth delay was associated with reduced intracellular ATP levels and increased antibiotic persistence. Using phosphopeptide enrichment and mass spectrometry-based proteomics, we identified possible targets of Ser/Thr phosphorylation that regulate cellular processes and bacterial growth, such as ribosomal proteins including the essential translation elongation factor EF-G. Finally, we show that acid stress leads to a reduced translational activity in the stp deletion mutant indicating metabolic quiescence correlating with increased antibiotic persistence.

scholarly journals Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling

2019 ◽  
Author(s):  
Bilal El Houdaigui ◽  
Raphaël Forquet ◽  
Thomas Hindré ◽  
Dominique Schneider ◽  
William Nasser ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Bacterial Genome ◽  
Transcriptional Regulator ◽  
Dna Supercoiling ◽  
Mechanistic Modeling ◽  
Mechanical Constraints ◽  
A Genome ◽  
Specific Regulation

AbstractDNA supercoiling acts as a global transcriptional regulator in bacteria, that plays an important role in adapting their expression programme to environmental changes, but for which no quantitative or even qualitative regulatory model is available. Here, we focus on spatial supercoiling heterogeneities caused by the transcription process itself, which strongly contribute to this regulation mode. We propose a new mechanistic modeling of the transcription-supercoiling dynamical coupling along a genome, which allows simulating and quantitatively reproducing in vitro and in vivo transcription assays, and highlights the role of genes’ local orientation in their supercoiling sensitivity. Consistently with predictions, we show that chromosomal relaxation artificially induced by gyrase inhibitors selectively activates convergent genes in several enterobacteria, while conversely, an increase in DNA supercoiling naturally selected in a long-term evolution experiment with Escherichia coli favours divergent genes. Simulations show that these global expression responses to changes in DNA supercoiling result from fundamental mechanical constraints imposed by transcription, independently from more specific regulation of each promoter. These constraints underpin a significant and predictable contribution to the complex rules by which bacteria use DNA supercoiling as a global but fine-tuned transcriptional regulator.

scholarly journals Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling

2019 ◽  
Vol 47 (11) ◽  
pp. 5648-5657 ◽  
Author(s):  
Bilal El Houdaigui ◽  
Raphaël Forquet ◽  
Thomas Hindré ◽  
Dominique Schneider ◽  
William Nasser ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Bacterial Genome ◽  
Transcriptional Regulator ◽  
Dna Supercoiling ◽  
Mechanistic Modeling ◽  
Mechanical Constraints ◽  
A Genome ◽  
Specific Regulation

Abstract DNA supercoiling acts as a global transcriptional regulator in bacteria, that plays an important role in adapting their expression programme to environmental changes, but for which no quantitative or even qualitative regulatory model is available. Here, we focus on spatial supercoiling heterogeneities caused by the transcription process itself, which strongly contribute to this regulation mode. We propose a new mechanistic modeling of the transcription-supercoiling dynamical coupling along a genome, which allows simulating and quantitatively reproducing in vitro and in vivo transcription assays, and highlights the role of genes’ local orientation in their supercoiling sensitivity. Consistently with predictions, we show that chromosomal relaxation artificially induced by gyrase inhibitors selectively activates convergent genes in several enterobacteria, while conversely, an increase in DNA supercoiling naturally selected in a long-term evolution experiment with Escherichia coli favours divergent genes. Simulations show that these global expression responses to changes in DNA supercoiling result from fundamental mechanical constraints imposed by transcription, independently from more specific regulation of each promoter. These constraints underpin a significant and predictable contribution to the complex rules by which bacteria use DNA supercoiling as a global but fine-tuned transcriptional regulator.

scholarly journals Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition

2021 ◽  
Vol 17 (5) ◽  
pp. e1008528
Author(s):  
Christian Schulz ◽  
Tjasa Kumelj ◽  
Emil Karlsen ◽  
Eivind Almaas
Keyword(s):  
Environmental Conditions ◽  
Model Performance ◽  
Optimal Growth ◽  
Metabolic Model ◽  
Biomass Composition ◽  
Metabolic Modelling ◽  
Composition Variation ◽  
Nutrient Environment ◽  
Genome Scale

Genome-scale metabolic modeling is an important tool in the study of metabolism by enhancing the collation of knowledge, interpretation of data, and prediction of metabolic capabilities. A frequent assumption in the use of genome-scale models is that the in vivo organism is evolved for optimal growth, where growth is represented by flux through a biomass objective function (BOF). While the specific composition of the BOF is crucial, its formulation is often inherited from similar organisms due to the experimental challenges associated with its proper determination. A cell’s macro-molecular composition is not fixed and it responds to changes in environmental conditions. As a consequence, initiatives for the high-fidelity determination of cellular biomass composition have been launched. Thus, there is a need for a mathematical and computational framework capable of using multiple measurements of cellular biomass composition in different environments. Here, we propose two different computational approaches for directly addressing this challenge: Biomass Trade-off Weighting (BTW) and Higher-dimensional-plane InterPolation (HIP). In lieu of experimental data on biomass composition-variation in response to changing nutrient environment, we assess the properties of BTW and HIP using three hypothetical, yet biologically plausible, BOFs for the Escherichia coli genome-scale metabolic model iML1515. We find that the BTW and HIP formulations have a significant impact on model performance and phenotypes. Furthermore, the BTW method generates larger growth rates in all environments when compared to HIP. Using acetate secretion and the respiratory quotient as proxies for phenotypic changes, we find marked differences between the methods as HIP generates BOFs more similar to a reference BOF than BTW. We conclude that the presented methods constitute a conceptual step in developing genome-scale metabolic modelling approaches capable of addressing the inherent dependence of cellular biomass composition on nutrient environments.

Garlic Extract (Allium sativum L.) Effectively Inhibits Staphylococcus aureus and Escherichia coli by Invitro Test

2020 ◽  
Vol 2 (2) ◽  
pp. 61-68
Author(s):  
Agnina Listya Anggraini ◽  
Ratih Dewi Dwiyanti ◽  
Anny Thuraidah
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Bacterial Infections ◽  
Allium Sativum ◽  
Antibacterial Properties ◽  
Herbal Medicines ◽  
Garlic Extract ◽  
Dilution Method ◽  
Initial Stage

Infection is a disease caused by the presence of pathogenic microbes, including Staphylococcus aureus and Escherichia coli. Garlic (Allium sativum L.) has chemical contents such as allicin, alkaloids, flavonoids, saponins, tannins, and steroids, which can function as an antibacterial against Staphylococcus aureus and Escherichia coli. This study aims to determine the antibacterial properties of garlic extract powder against Staphylococcus aureus and Escherichia coli. This research is the initial stage of the development of herbal medicines to treat Staphylococcus aureus and Escherichia coli infections. The antibacterial activity test was carried out by the liquid dilution method. The concentrations used were 30 mg/mL, 40 mg/mL, 50 mg/mL, 60 mg/mL and 70 mg/mL. The results showed that the Minimum Inhibitory Concentration (MIC) against Staphylococcus aureus and Escherichia coli was 40 mg/mL and 50 mg / mL. Minimum Bactericidal Concentration (MBC) results for Staphylococcus aureus and Escherichia coli are 50 mg/mL and 70 mg/mL. Based on the Simple Linear Regression test, the R2 value of Staphylococcus aureus and Escherichia coli is 0.545 and 0.785, so it can be concluded that there is an effect of garlic extract powder on the growth of Staphylococcus aureus and Escherichia coli by 54.5% and 78.5%. Garlic (Allium sativum L.) extract powder has potential as herbal medicine against bacterial infections but requires further research to determine its effect in vivo.

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