Systems biology investigation of aromatic compound catabolism in facultative anaerobic Aromatoleum aromaticum EbN1T
DownloadMembers of the genus Aromatoleum are cosmopolitan in diverse habitats and utilize a broad range of recalcitrant organic molecules coupled to denitrification or O2-respiration. To gain a holistic understanding of the model organism A. aromaticum EbN1T, we here studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate and acetate utilized under nitrate-reducing vs. oxic conditions. Multi-OMICS (transcriptome, proteome and metabolome) covered the catabolic network (199 genes) to the largest part and allowed refining the knowledge on the studied degradation modules. Their substrate-dependent regulation showed differing degrees of specificity ranging from high with 3-(4-hydroxyphenyl)propanoate to mostly relaxed with benzoate. For benzoate, transcript and protein formation was essentially constitutive, contrasted by anoxia- vs. oxia-specific metabolite profiles. Matrix factorization of transcriptomic data revealed the anaerobic modules to account for most of the variance across the degradation network. The respiratory network appeared constitutive both on transcript and protein level, except for nitrate reductase (narGHI expression occurring only under nitrate-reducing conditions). Anoxia/nitrate-dependent transcription of denitrification genes is apparently controlled by three FNR-type regulators as well as NarXL (all constitutively formed). Re-sequencing and functional re-annotation of the genome fostered a genome-scale metabolic model, which comprises 655 enzyme-catalyzed reactions and 731 distinct metabolites. The model predictions for growth rates and biomass yields agreed well with experimental stoichiometric data, except for 3-(4-hydroxyphenyl)propanoate, where 4-hydroxybenzoate was exported. Taken together the combination of multi-OMICS, growth physiology and metabolic model advanced our knowledge of a relevant environmental microorganism that differs significantly from other bacterial model strains.
DOI: 10.15490/fairdomhub.1.investigation.534.1
Zenodo URL: None
Created at: 15th Oct 2022 at 20:00
Experimental multi-OMICS
No description specified
CoA LC/MS Data
No description specified
CoA LC/MS Data Sample Identification
No description specified
- Metabolite profiling template_CoA-esters.xlsx
Cultivation for multi-OMICS
Harvest optical densites and methods of transcriptom, proteom and metabolom samples for all tested substrat conditions.
SOP – Substrate adaptation, cultivation and harvesting for multi-OMICS analysis
No description specified
- SOP – Substrate adaptation, cultivation and harvesting for multi-OMICS analysis.pdf
non-volatile metabolites GC/MS
No description specified
Results - Non-volatile, small, polar metabolites via GC-MS
No description specified
- results_non-volatile_metabolites_GC-MS.xlsx
Non-volatile, small, polar metabolites´GC/MS data sample identification
No description specified
- Metabolite profiling template_small_metabolites.xlsx
SOP - Extraction of non-volatile, small, polar metabolites for GC-MS analysis
No description specified
- SOP_extraction_non-volatile_metabolites.pdf
SOP - Analysis of non-volatile, small, polar metabolites via GC-MS
No description specified
- SOP_analysis_non-volatile_metabolites.pdf
SOP - Data evaluation of non-volatile, small, polar metabolites
No description specified
- SOP_data_evaluation_non-volatile_metabolites.pdf
Transcriptomic data
No description specified
Proteomic data
No description specified
Detailed peptide data for identified proteins
No description specified
- Aromatoleum aromaticum EbN1 peptide data.rar
SOP – Protein preparation, nanoLC-MS/MS analyses of peptides and protein identification
No description specified
- SOP – Protein preparation analysis and identification.pdf
Genome re-annotation
No description specified
EbN1 Genome re-annotation
No description specified
Aromatoleum aromaticum EbN1 chromosome, complete sequence
No description specified
- Aromatoleum aromaticum EbN1 chromosome 2022 complete sequence.gb
Aromatoleum aromaticum EbN1 plasmid1, complete sequence
No description specified
- Aromatoleum aromaticum EbN1 plasmid1 2022 complete sequence.gb
Aromatoleum aromaticum EbN1 plasmid2, complete sequence
No description specified
- Aromatoleum aromaticum EbN1 plasmid2 2022 complete sequence.gb
Metabolic Modelling
No description specified
Scenario files for Metano metabolic modeling
All files for metabolic modeling using the Metano toolbox, including the scenarios and flux balance analyses.
Model - Scenario - Acetate aerobic
The metano scenario file for aerobic growth on acetate.
- sce_Ac_aerobic.txt
Model - Scenario - Acetate anaerobic
The metano scenario file for anaerobic growth on acetate.
- sce_Ac_anaerobic.txt
Model - Scenario - Benzoate aerobic
The metano scenario file for aerobic growth on Benzoate.
- sce_Bz_aerobic.txt
Model - Scenario - Benzoate anaerobic
The metano scenario file for anaerobic growth on benzoate.
- sce_Bz_anaerobic.txt
Model - Scenario - Phenylalanine aerobic
The metano scenario file for aerobic growth on L-phenylalanine.
- sce_Phe_aerobic.txt
Model - Scenario - Phenylalanine anaerobic
The metano scenario file for anaerobic growth on L-phenylalanine.
- sce_Phe_anaerobic.txt
Model - Scenario - 3-HBz aerobic
The metano scenario file for aerobic growth on 3-Hydroxybenzoate.
- sce_3HBz_aerobic.txt
Model - Scenario - 3-HBz anaerobic
The metano scenario file for anaerobic growth on 3-Hydroxybenzoate.
- sce_3HBz_anaerobic.txt
Model - Scenario - 4HPP aerobic
The metano scenario file for aerobic growth on 4HPP.
- sce_4HPP_aerobic.txt
Model - Scenario - 4HPP anaerobic
The metano scenario file for anaerobic growth on 4HPP.
- sce_4HPP_anaerobic.txt
EbN1 stoichiometric model iAA835 (Metano)
This stoichiometric model of Aromatoleum aromaticum EbN1 is a genome-scale model and comprises 655 enzyme-catalyzed reactions and 731 distinct metabolites.
The model is in the plain-text reaction format of Metano that is human-readable and can be opened with every text editor.
To run this version of the model, please use the Metano Modeling Toolbox (mmtb.brenda-enzymes.org) and the associated scenario files.
- model_iAA835.txt
Metabolic modeling of EbN1
All flux balance analyses of the stoichiometric model
Model | Flux balance analysis (FBA)
Comparative flux balance analysis file. All values are given in mmol/g/h. Fluxes were optimized to maximize BIOMASS.
- Fluxes.xlsx
Model | Simulation parameters and results
Uptake and growth rates, and biomass yields are compared in vivo and in silico.
- Simulations.xlsx
EbN1 stoichiometric model iAA835 (Metano)
This stoichiometric model of Aromatoleum aromaticum EbN1 is a genome-scale model and comprises 655 enzyme-catalyzed reactions and 731 distinct metabolites.
The model is in the plain-text reaction format of Metano that is human-readable and can be opened with every text editor.
To run this version of the model, please use the Metano Modeling Toolbox (mmtb.brenda-enzymes.org) and the associated scenario files.
- model_iAA835.txt
EbN1 stoichiometric model iAA835 (SBML)
Stoichiometric model in SBML format using the acetate-aerobic standard scenario.
Please note that SBML was exported using the sbmlwriter class of Metano. This file was not used for the actual analyses.
- iAA835.sbml
Model | Supplementary table
Supplementary table containing all reactions, genes, and metabolites involved in the metabolic model iAA835 .
- model_iAA835.xlsx
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Created: 15th Oct 2022 at 20:00
Last updated: 16th Oct 2022 at 05:53
