Chemoproteomic Profiling of Bile Acid Interacting Proteins

Abstract

Bile acids (BAs) are a family of endogenous metabolites synthesized from cholesterol in liver and modified by microbiota in gut. Being amphipathic molecules, the major function of BAs is to help with dietary lipid digestion. In addition, they also act as signaling molecules to regulate lipid and glucose metabolism as well as gut microbiota composition in the host. Remarkably, recent discoveries of the dedicated receptors for BAs such as FXR and TGR5 have uncovered a number of novel actions of BAs as signaling hormones which play significant roles in both physiological and pathological conditions. Disorders in BAs’ metabolism are closely related to metabolic syndrome and intestinal and neurodegenerative diseases. Though BA-based therapies have been clinically implemented for decades, the regulatory mechanism of BA is still poorly understood and a comprehensive characterization of BA-interacting proteins in proteome remains elusive. We herein describe a chemoproteomic strategy that uses a number of structurally diverse, clickable, and photoreactive BA-based probes in combination with quantitative mass spectrometry to globally profile BA-interacting proteins in mammalian cells. Over 600 BA-interacting protein targets were identified, including known endogenous receptors and transporters of BA. Analysis of these novel BA-interacting proteins revealed that they are mainly enriched in functional pathways such as endoplasmic reticulum (ER) stress response and lipid metabolism, and are predicted with strong implications with Alzheimer’s disease, non-alcoholic fatty liver disease, and diarrhea. Our findings will significantly improve the current understanding of BAs’ regulatory roles in human physiology and diseases.

Chemical Reporters for Exploring Microbiology and Microbiota Mechanisms

“…[78] D) Bile acid photoaffinity reporters. [81] employeda ctivity-based probes/reporters in combination with candidate inhibitor screening and discovered novel inhibitors of bacterial proteases that are important for the virulence of challenging and drug-resistant pathogens such as C. difficile [92] and S. aureus. [93] These select examples highlight how ABPP reporters are excellent tools for profiling of specific protein families involved fundamental microbial physiology as well as the discovery and development of new antimicrobial agents.…”

“…[120][121][122] These exciting studies suggests pecific microbiota speciesm ight generate unique metabolites to alter host immunity or infection, but the protein targets and mechanism(s) of action for these microbiota-derived metabolites in host cells and/or microbes have not been fully characterized, thus could benefit from future studies with chemical reporters. Indeed, photoaffinity reportersh ave been previously generated for fatty acids (Figure 10 C), [78] cholesterol [123] and bilea cids [81] (Figure 10 D) and could be readily developed for otherm icrobiota-associated metabolites.…”

Activity-Based Protein Profiling—Enabling Multimodal Functional Studies of Microbial Communities

“…Recently, Lei and colleagues developed bile acid-derived photoreactive probes (Zhuang et al 2017). Using a competition-based approach, they identified known and novel bile acid-interacting proteins in HeLa cells including carnitine palmitoyl transferase 1A (CPT1A) and ADP-dependent glucokinase (ADPGK).…”

Color‐Tunable Light‐up Bioorthogonal Probes for In Vivo Two‐Photon Fluorescence Imaging

“…During the past few years, considerable efforts have been made toward extracellular or intracellular turn‐on bioimaging with azide or tetrazine fluorogenic probes in living cells . These probes could undergo bioorthogonal reaction by copper‐catalyzed (CuAAc) or Diels–Alder cycloaddition, respectively .…”