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.