Photo-ANA enables profiling of host–bacteria protein interactions during infection

Bacterial pathogens rapidly change and adapt their proteome to cope with the environment in host cells and secret effector proteins to hijack host targets to ensure their survival and proliferation during infection. Excessive host proteins make it difficult to profile pathogens’ proteome dynamics by conventional proteomics. It is even more challenging to map pathogen-host protein-protein interactions in real time, given the low abundance of bacterial effectors and weak and transient interactions they may be involved. Here, we report a method for selectively labeling of bacterial proteome using a bifunctional amino acid, photo-ANA, equipped with a bioorthogonal handle and a photoreactive warhead, which enables simultaneous analysis of bacterial proteome reprogramming and pathogen-host protein interactions of Salmonella Typhimurium during infection. Using photo-ANA, we discovered temporal and distinct protein synthesis changes inside host cells and identified FLOT1/2 as the novel host interactors of Salmonella Typhimurium effector PipB2 in late stage of infection.