Biology subjects

Spadiut, O.

Publications and source records attributed to Spadiut, O..

3 recordsLinked to original sources

bioRxiv2025

A moss N-Acetyltransferase-MAPK protein controls 2D to 3D developmental transition via acetylation and phosphorylation changes

Post-translational modifications (PTMs) finetune plant responses to developmental and environmental cues by impacting protein activity, stability, localization and interaction landscape. In this study we identified a moss specific protein which combines two common PTMs: acetylation and phosphorylation. This protein originated from the fusion of a MAPK with an N-acetyltransferase, for which we named it Rosetta NATD-MAPK 1 (RAK1). Using biochemical methods, we demonstrated that RAK1 has acetyltransferase activity that is enhanced by activation of its MAPK domain. Phenotypical studies of rak1 knockout mutants revealed a role for RAK1 in the regulation of the 2D-to-3D growth transition. Through Mass Spectrometry we verified that defective 2D-to-3D transition in the mutants was caused by differentially regulated acetylation and phosphorylation events associated to metabolic reprogramming and 3D differentiation. Collectively, this study uncovers a previously unknown multidomain protein and provides insights into the interplay of PTMs during developmental reprogramming. TeaserAcetylation and phosphorylation changes modulate the 2D to 3D developmental transition in Physcomitrium patens.

plant biology↗

bioRxiv2024

Optimizing Bioprocessing Efficiency with OptFed: Dynamic Nonlinear Modeling Improves Product-to-Biomass Yield by 19%

Biotechnological production of recombinant molecules relies heavily on fed-batch processes. However, as the cells growth, substrate uptake, and production kinetics are often unclear, the fed-batches are frequently operated under sub-optimal conditions. Process design is based on simple feed profiles (e.g., constant or exponential), operator experience, and basic statistical tools (e.g., response surface methodology), which are unable to harvest the full potential of production. To address this challenge, we propose a general modeling framework, OptFed, which utilizes experimental data from non-optimal fed-batch processes to predict an optimal one. In detail, we assume that cell-specific rates depend on several state variables and their derivatives. Using measurements of bioreactor volume, biomass, and product, we fit the kinetic constants of ordinary differential equations. A regression model avoids overfitting by reducing the number of parameters. Thereafter, OptFed predicts optimal process conditions by solving an optimal control problem using orthogonal collocation and nonlinear programming. In a case study, we apply OptFed to a recombinant protein L fed-batch production process. We determine optimal controls for feed rate and reactor temperature to maximize the product-to-biomass yield and successfully validate our predictions experimentally. Notably, our framework outperforms RSM in both simulation and experiments, capturing an optimum previously missed. We improve the experimental product-to-biomass ratio by 19 % and showcase OptFeds potential for enhancing process optimization in biotechnology.

bioengineering↗

bioRxiv2022

N-linked glycosylation increases horse radish peroxidase rigidity leading to enhanced activity and stability.

Glycosylation is the most prevalent protein post-translational modification, with a quarter of glycosylated proteins having enzymatic properties. Yet the full impact of glycosylation on the protein structure-function relationship, especially in enzymes, is still limited. Here we show glycosylation rigidifies the important commercial enzyme horseradish peroxidase (HRP), which in turn increases its activity and stability. Circular dichroism spectroscopy revealed that glycosylation increased holo-HRPs thermal stability and promoted significant helical structure in the absence of haem (apo-HRP). Glycosylation also resulted in a 10-fold increase in enzymatic turnover towards o-phenylenediamine dihydrochloride when compared to its non-glycosylated form. Utilising a naturally occurring site-specific probe of active site flexibility (Trp117) in combination with red-edge excitation shift fluorescence spectroscopy, we found that glycosylation significantly rigidified the enzyme. In silico simulations confirmed that glycosylation largely decreased protein backbone flexibility, especially in regions close to the active site and the substrate access channel. Thus, our data shows that glycosylation does not just have a passive effect on HRP stability but can exert long range effects that mediate the native enzymes activity and stability through changes in inherent dynamics.

biochemistry↗