Activity-based protein profiling of chitin catabolism

Abstract

Microbial catabolism of chitin, a highly abundant component of polymeric organic matter worldwide, is a fundamental cog in the carbon and nitrogen cycles that govern CO2 emissions, nutrient dynamics in aquatic systems, and soil vitality. Despite this critical biogeochemical function, we have a poor understanding of the synergy between various microbial chitinases and key accessory enzymes involved in chitin catabolism. We designed and synthesized activity-based probes (ABPs) for profiling active chitinolytic enzymes by modifying the chitin derivatives N-acetyl glucosamine and chitotriose. The ABPs were used to determine the active complement of chitinolytic enzymes produced over time by the soil bacterium Cellvibrio japonicus treated with various C substrates. This approach allowed us to demonstrate the utility of these ABPs in determining the intricate synergy between chitinases and other glycoside hydrolases that microbes employ to catabolize chitin. The strategy can be used to gain molecular level insights that can be used to better understand microbial roles in soil C and N cycling in the face of a changing climate.