P5: The FAIR kinetic characterization of CoaBC from Staphylococcus aureus
Many experimental procedures in biochemical laboratory practice are repetitive, time-consuming, and prone to human error due to manual processing. One procedure is the spectrophotometric assay for analysing enzymatic activity using microtiter plates. Currently, transferring experimental data from the instrument to the analysis platform requires manual copying and pasting. Recently, a specialized markup language EnzymeML and the associated PyEnzyme software were created to automate parts of this workflow, specifically fitting models to experimental data and transferring kinetic parameters to databases. However, the programming of the experimental protocol and the transfer of metadata have not yet been automated. Moreover, in enzymology research, scientists are frequently facing reproducibility issues, mainly because crucial metadata are not reported. These can include the precise reaction conditions, comprehensive experimental results, and procedures used for data analysis. Therefore, the aim of this study was to implement and test tools and interfaces to automate aspects of the experimental workflow and associated data management. These interfaces will assist in enabling data to be Findable, Accessible, Interoperable and Reusable (FAIR). The tools are tested in the laboratory by performing enzymatic assays using an OT2 liquid handler to characterize the bi-functional enzyme complex consisting of phosphopantothenoylcysteine synthetase and phophopantothenoylcysteiene decarboxylase (CoaBC), the second and third enzymes in the coenzyme A biosynthesis pathway. In Staphylococcus aureus, CoaBC has not yet been kinetically characterised; this process is extremely challenging due to the complexity of the enzyme system, as it involves multiple substrates, products and sequential reactions. To mitigate this, we aim to link the activity of CoaBC to the activity of the fourth enzyme CoaD, which is responsible for catalysing the conversion of 4’-phosphopantetheine to dephospho-Coenzyme A with the release of pyrophosphate. The kinetics of the first step catalysed by CoaBC and the kinetics of CoaD were investigated by measuring the production of pyrophosphate in an enzyme-linked assay. During the second step of the reaction catalysed by CoaBC, CO2 is released, which cannot be measured spectrophotometrically. Therefore, we aim to perform kinetic assays either with CoaBC on its own, or by combining both enzymes CoaBC and CoaD. In the case where we combine both enzymes, we expect the rate to be twice as fast, since two pyrophosphate molecules are released compared to the case with only CoaBC where only one pyrophosphate is released. Lastly, we construct a kinetic model using PySCeS, where datasets with CoaBC and CoaD and datasets without CoaD are combined and the kinetic parameters for previously obtained for the first step of CoaBC and CoaD are included, to fit the kinetic parameter values for the second step catalysed by CoaBC.