Biology subjects

Kummer, U.

Publications and source records attributed to Kummer, U..

3 recordsLinked to original sources

bioRxiv2021

All driven by energy demand? Integrative comparison of metabolism of Enterococcus faecalis wildtype and a glutamine synthase mutant

Lactic acid bacteria (LAB) play a significant role in biotechnology, e.g. food industry, but also in human health. Many LAB genera have developed a multidrug resistance in the past few years, becoming a serious problem in controlling hospital germs all around the world. Enterococcus faecalis accounts for a large part of the human infections caused by LABs. Therefore, studying its adaptive metabolism under various environmental conditions is particularly important. In this study, we investigated the effect of glutamine auxotrophy ({Delta}glnA mutant) on metabolic and proteomic adaptations of E. faecalis in response to a changing pH in its environment. Changing pH values are part of its natural environment in the human body, but also play a role in food industry. We compared the results to those of the wildtype. Our integrative method, using a genome-scale metabolic model, constrained by metabolic and proteomic data allows us to understand the bigger picture of adaptation strategies in this bacterium. The study showed that energy demand is the decisive factor in adapting to a new environmental pH. The energy demand of the mutant was higher at all conditions. It has been reported that {Delta}glnA mutants of bacteria are energetically less effective. With the aid of our data and model we are able to explain this phenomenon as a consequence of a failure to regulate glutamine uptake and the costs for the import of glutamine and the export of ammonium. Methodologically, it became apparent that taking into account the non-specificity of amino acid transporters is important for reproducing metabolic changes with genome-scale models since it affects energy balance.

systems biology↗

bioRxiv2021

Integration of computational modeling and quantitative cell physiology reveals central parameters for the brassinosteroid-regulated elongation growth along the axis of the Arabidopsis root

Brassinosteroids (BR) are key hormonal regulators of plant development. However, whereas the individual components of BR perception and signaling are well characterized experimentally, the question of how they can act and whether they are sufficient to carry out the critical function of cellular elongation remains open. Here, we combined computational modeling with quantitative cell physiology to understand the dynamics of the plasma membrane (PM)-localized BR response pathway during the initiation of cellular responses in the epidermis of the Arabidopsis root tip that are be linked to cell elongation. The model, consisting of ordinary differential equations, comprises the BR induced hyperpolarization of the PM, the acidification of the apoplast and subsequent cell wall swelling. We demonstrate that the competence of the root epidermal cells for the BR response predominantly depends on the amount and activity of H+-ATPases in the PM. The model further predicts that an influx of cations is required to compensate for the shift of positive charges caused by the apoplastic acidification. A potassium channel was subsequently identified and experimentally characterized, fulfilling this function. Thus, we established the landscape of components and parameters for physiological processes potentially linked to cell elongation, a central process in plant development.

plant biology↗

bioRxiv2020

Impact of explicit area scaling on kinetic models involving multiple compartments

BackgroundComputational modelling of cell biological processes is a frequently used technique to analyse the underlying mechanisms and to generally understand the behaviour of these processes in the context of a pathway, network or even the whole cell. The most common technique in this context is the usage of ordinary differential equations (ODEs) that describe the kinetics of the relevant processes in mechanistic detail. Here, it is usually assumed that the content of the cell is well-stirred and thus homogeneous - which is of course an over-simplification, but often worked in the past. However, many processes happen at membranes and thus not in 3D, but in 2D. The scaling of the rates of these processes poses a special problem, if volumes of compartments are changed. They will typically scale with an area, but not with the volume of the involved compartment. However, commonly, this is neglected when setting up models and/or volume scaling also sometimes automatically happens when using modelling software in the field. ResultsHere, we investigate generic as well as specific, realistic cases to find out, how strong the impact of the wrong scaling is for the outcome of simulations. We show that the importance of correct area scaling depends on the architecture of the reaction site and its changes upon volume alterations and it is hard to foresee, if it has a significant impact or not just by looking at the original model set-up. Moreover, scaled rates might exhibit more or less control over the behaviour of the system and therefore, accordingly, incorrect scaling will have more or less influence. ConclusionsWorking with multi-compartment reactions requires a careful consideration of the correct scaling of the rates when changing the volumes of the involved compartments. The error following incorrect scaling - often done by scaling with the volume of the respective compartments can lead to significant aberrations of model behaviour.

systems biology↗