Systems biology investigation of aromatic compound catabolism in facultative anaerobic Aromatoleum aromaticum EbN1T

Members 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

Contents

Experimental multi-OMICS

No description specified

CoA LC/MS Data

No description specified

NO3_MS_CoA_Data

No description specified

  • NO3_MS_CoA_Data.zip

O2_MS_CoA_Data

No description specified

  • O2_MS_CoA_Data.zip

Results - CoA-esters via LC-MS

No description specified

  • results_CoA-esters_LC-MS.xlsx

CoA LC/MS Data Sample Identification

No description specified

  • Metabolite profiling template_CoA-esters.xlsx

SOP_extraction_CoA-esters

No description specified

  • SOP_extraction_CoA-esters.pdf

SOP_analysis_CoA-esters

No description specified

  • SOP_analysis_CoA-esters.pdf

SOP_data_evalutation_CoA-esters

No description specified

  • SOP_data_evaluation_CoA-esters.pdf

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

NO3_MS_small_metabolites_Data

No description specified

  • NO3_MS_small_metabolites_Data.zip

O2_MS_small_metabolites_Data

No description specified

  • O2_MS_small_metabolites_Data.zip

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

EbN1 fastq Bz

No description specified

  • EbN1_fastq_Bz.zip

EbN1 fastq 3HBz

No description specified

  • EbN1_fastq_3HBz.zip

EbN1 fastq 4HPP

No description specified

  • EbN1_fastq_4HPP.zip

EbN1 fastq Phe

No description specified

  • EbN1_fastq_Phe.zip

EbN1 fastq Ac

No description specified

  • EbN1_fastq_Ac.zip

Proteomic data

No description specified

Protein identification data

No description specified

  • Aromatoleum aromaticum EbN1 protein data.rar

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 | Biomass composition

No description specified

  • Biomass_iAA835.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
Fingerprints

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MD5: 13e99c50e569579a70f7f18c4af2386d

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Citation
Neumann-Schaal, M., & Becker, P. (2022). Systems biology investigation of aromatic compound catabolism in facultative anaerobic Aromatoleum aromaticum EbN1T. FAIRDOMHub. https://doi.org/10.15490/FAIRDOMHUB.1.INVESTIGATION.534.1
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Created: 15th Oct 2022 at 20:00

Last updated: 16th Oct 2022 at 05:53

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