Biochemistry

Peptidoglycan (PG), a network of glycan strands crosslinked by short peptides, is an essential and bacterial-specific structure that determines cell shape and protects cells from lysis. Understanding how bacteria assemble, maintain, and modify their PG not only addresses fundamental questions in cell biology but also provides a basis for developing strategies to treat bacterial infections. Although several in vitro methods, such as zymography, Remazol Brilliant Blue (RBB) assay, and LC-MS analyses, are available to quantify the activities of PG-modification enzymes, these approaches are not readily applicable in vivo. Here, we describe a single-particle tracking photo-activated localization microscopy (sptPALM)-based method to quantify the binding of enzymes to PG in vivo, which serves as a proxy for their enzymatic activities. Because the PG meshwork is relatively immobile, fluorescently tagged enzymes that transiently or stably bind it exhibit reduced mobility, reflected by lower diffusion coefficients. This approach provides sensitive, quantitative, and real-time insights into enzyme behavior in vivo under diverse physiological conditions or genetic backgrounds. The protocol is particularly valuable for investigating PG-modification enzymes that are essential or functionally redundant, which are often difficult to analyze using traditional genetic methods.