Exploring metalloproteome remodeling in calprotectin-stressed Acinetobacter baumannii using chemoproteomics

The growth of bacterial pathogens is limited by nutritional immunity, where the infected host deploys metal scavenging proteins to starve the pathogen of essential transition metals. An important transition metal-sequestering protein is the S100A8-S100A9 heterotetramer, calprotectin (CP). Prior work reveals that CP induces a significant Zn- and Fe-starvation response in the Gram-negative opportunistic pathogen, Acinetobacter baumannii, in liquid culture. Here, we employ a quantitative chemoproteomics platform to pinpoint changes in abundance-corrected cysteine reactivity, and by extension cellular metal occupancy in metalloenzymes, that occur when A. baumannii is challenged with physiological CP in liquid culture relative to an untreated WT control. Changes in protein abundance with CP stress reveal a pronounced Zn-limitation and Fe-starvation response and reciprocal regulation of three enzymes of central carbon metabolism, including aconitase. A majority of the 2645 quantifiable Cys-containing peptides that show an increase in abundance-corrected Cys reactivity (150) are derived from known Zn-, Fe- and Fe-S-cluster proteins, revealing a significant decrease in metal occupancy (undermetalation) across the proteome. Myriad cell processes are compromised by undermetalation of the metalloproteome, including enzymes that function in the TCA cycle and respiration, GTP metabolism, ribosome remodeling, tRNA charging, and proteostasis. A direct comparison of a strain lacking the candidate metallochaperone ZigA (ΔzigA) with the wild-type strain reveals that the loss of ZigA is effectively silent in this assay. We conclude that CP induces a widespread, negative impact on the metalation status of the metalloproteome that results in a significant nutrient limitation response.