Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic EbN1.

Members of the genus thrive in diverse habitats and use a broad range of recalcitrant organic molecules coupled to denitrification or O respiration. To gain a holistic understanding of the model organism EbN1, we studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate, and acetate utilized under nitrate-reducing versus oxic conditions. Integrated multi-omics (transcriptome, proteome, and metabolome) covered most of the catabolic network (199 genes) and allowed for the refining of knowledge of the degradation modules studied.

The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases.

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes.

Fixation of CO using the ethylmalonyl-CoA pathway in the photoheterotrophic marine bacterium Dinoroseobacter shibae.

The ability of aerobic anoxygenic photoheterotrophs (AAPs) to gain additional energy from sunlight represents a competitive advantage, especially in conditions where light has easy access or under environmental conditions may change quickly, such as those in the world´s oceans. However, the knowledge about the metabolic consequences of aerobic anoxygenic photosynthesis is very limited. Combining transcriptome and metabolome analyses, isotopic labelling techniques, measurements of growth, oxygen uptake rates, flow cytometry, and a number of other biochemical analytical techniques we obtained a comprehensive overview on the complex adaption of the marine bacterium Dinoroseobacter shibae DFL12 during transition from heterotrophy to photoheterotrophy (growth on succinate).

A metabolite-centric view on flux distributions in genome-scale metabolic models.

Background: Genome-scale metabolic models are important tools in systems biology. They permit the in-silico prediction of cellular phenotypes via mathematical optimisation procedures, most importantly flux balance analysis. Current studies on metabolic models mostly consider reaction fluxes in isolation.

Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus.

We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon Sulfolobus solfataricus, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2-4 (optimum 3.5) and a temperature of 75-80°C (optimum 80°C).

Tracing catalytic conversion on single zeolite crystals in 3D with nonlinear spectromicroscopy.

The cost- and material-efficient development of next-generation catalysts would benefit greatly from a molecular-level understanding of the interaction between reagents and catalysts in chemical conversion processes. Here, we trace the conversion of alkene and glycol in single zeolite catalyst particles with unprecedented chemical and spatial resolution. Combined nonlinear Raman and two-photon fluorescence spectromicroscopies reveal that alkene activation constitutes the first reaction step toward glycol etherification and allow us to determine the activation enthalpy of the resulting carbocation formation.