Profiling the Heme-Binding Proteomes of Bacteria Using Chemical Proteomics

Heme is a cofactor with myriad roles and essential to almost all living organisms. Beyond classical gas transport and catalytic functions, heme is increasingly appreciated as a tightly controlled signalling molecule regulating protein expression. However, heme acquisition, biosynthesis and regulation is poorly understood beyond a few model organisms, and the heme-binding proteome has not been fully characterised in bacteria. Yet as heme homeostasis is critical for bacterial survival, heme-binding proteins are promising drug targets. Herein we report a chemical proteomics method for global profiling of heme-binding proteins in live cells for the first time. Employing a panel of heme-based clickable and photoaffinity probes enabled the profiling of 32-54 % of the known heme-binding proteomes in Gram-positive and Gram-negative bacteria. This simple-to-implement profiling strategy could be interchangeably applied to different cell types and systems and fuel future research into heme biology.

Automated summary

Heme is a cofactor that plays myriad roles and is essential to almost all living organisms. It is now recognized as a tightly controlled signaling molecule that regulates protein expression. However, our understanding of heme acquisition, biosynthesis, and regulation is limited, especially in bacteria. In this study, a chemical proteomics method was developed to profile heme-binding proteins in live cells for the first time. This strategy successfully identified a significant portion of the heme-binding proteome in Gram-positive and Gram-negative bacteria and has the potential to fuel future research in heme biology.