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• W4315709577 abstract "Protein-protein interactions are the basis for many biological processes in the cell. Understanding these interactions is crucial for the general analysis of how the cell functions and the potential identification of novel therapeutical targets. Over the years, many different techniques have been developed to study these protein interactions, among them high throughput approaches such as crosslinking mass spectrometry and co-fractionation mass spectrometry. The combination of these approaches with the artificial intelligence-based protein conformation prediction tool AlphaFold allowed the identification of many novel protein complexes in B. subtilis, including complexes that involved proteins of unknown function. The aim of this work was to validate these novel protein interactions and to prove the functionality of this workflow. An additional objective was assigning functions to some of the so far understudied proteins that were identified in these complexes. The complexes between the pyruvate dehydrogenase and YneR, the iron sensor Fur and the essential protein of unknown function YlaN as well as the interaction of the paralogous protein YabR and YugI with the ribosome were studied intensively. YneR was identified as the first known inhibitor of the pyruvate dehydrogenase activity in B. subtilis, and therefore renamed to PdhI. This was achieved through growth experiments. Electrophoretic mobility shift assays showed that YlaN inhibits Fur-DNA binding activity. AlphaFold Multimer prediction revealed a potentially strong change in the conformation of the Fur dimer upon binding of YlaN. Furthermore, we showed that ylaN can be deleted, if fur had been deleted before. Together, these findings demonstrate that the essentiality of YlaN is due to the regulation of the DNA binding activity of Fur. The paralogous proteins YabR and YugI bind to the 30S subunit of the ribosome. This was validated via Western blot analysis of purified ribosomes and bacterial two-hybrid assays. Deletion of yabR affected growth on minimal medium and YugI seems to play a role in tetracycline susceptibility. It was suspected that both proteins perform the same essential function in the cell and can replace each other. This hypothesis could be refuted by the creation of a double deletion strain. To summarize, this work illustrates that the combination of the complementary techniques crosslinking mass spectrometry and co-fractionation mass spectrometry allows the accurate prediction of protein complexes in B. subtilis without the need for genetic manipulation of the organism. The validation of this concept led to the identification of the function of multiple proteins and the discovery of so far unknown regulatory mechanisms." @default.
• W4315709577 created "2023-01-12" @default.
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• W4315709577 date "2023-01-12" @default.
• W4315709577 modified "2023-10-14" @default.
• W4315709577 title "Validation of novel protein-protein interactions in Bacillus subtilis" @default.
• W4315709577 doi "https://doi.org/10.53846/goediss-9661" @default.
• W4315709577 hasPublicationYear "2023" @default.
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