A metabolic labeling strategy for relative protein quantification in Clostridioides difficile

Clostridioides difficile (formerly Clostridium difficile) is a Gram-positive, spore-forming pathogen which cases drug-induced Clostridioides difficile-associated diseases in hospitals worldwide. A detailed analysis of the proteome may provide new targets for drug development or therapy strategies to combat this pathogen. So far, quantitative proteome analyses could only be carried out by label-free or chemical labeling methods. However, the application of metabolic labeling would allow for accurate quantification of significant differences, even in the case of very small changes. Additionally, it would be possible to perform bias free studies of the membrane or surface proteome which require elaborated preparations and are therefore prone to higher standard deviations during the quantification. Up to now, the implementation of metabolic labeling strategies of C. difficile was hampered by the very specific metabolic requirements of this anaerobic pathogen. To solve this problem, media were evaluated and the cultivation procedure with 15N labeled media for the C. difficile 630Δerm strain was optimized to gain a high incorporation rate. In the following proof-of-principle experiment, the cytosolic sub-proteomes of C. difficile cells of three different cultivation media and two growth phases were analyzed resulting in reproducible data which are shown in detail.