Proteomic characterization of <i>Mycobacterium tuberculosis</i> subjected to carbon starvation

<i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) is the causative agent of tuberculosis (TB), the leading cause of infectious disease-related deaths worldwide. TB infections present on a spectrum from active to latent disease. In the human host, <i>Mtb</i> faces hostile environments, such as nutrient deprivation, hypoxia, and low pH. Under these conditions, <i>Mtb</i> can enter a dormant, but viable, state characterized by a lack of cell replication and increased resistance to antibiotics. Dormant <i>Mtb</i> poses a major challenge to curing infections and eradicating TB globally. We subjected <i>Mtb</i> mc²6020 (Δ<i>lysA</i> and Δ<i>panCD</i>), a double auxotrophic strain, to carbon starvation (CS), a culture condition that induces growth stasis and mimics environmental conditions associated with dormancy <i>in vivo</i>. We provide a detailed analysis of the proteome in CS compared to replicating samples. We observed extensive proteomic reprogramming, with 36% of identified proteins significantly altered in CS. Many enzymes involved in oxidative phosphorylation and lipid metabolism were retained or more abundant in CS. The cell wall biosynthetic machinery was present in CS, although numerous changes in the abundance of peptidoglycan, arabinogalactan, and mycolic acid biosynthetic enzymes likely result in pronounced remodeling of the cell wall. Many clinically approved anti-TB drugs target cell wall biosynthesis, and we found that these enzymes were largely retained in CS. Lastly, we compared our results to those of other dormancy models and propose that CS produces a physiologically distinct state of stasis compared to hypoxia in <i>Mtb</i>.IMPORTANCETuberculosis is a devastating human disease that kills over 1.2 million people a year. This disease is caused by the bacterial pathogen <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>). <i>Mtb</i> excels at surviving in the human host by entering a non-replicating, dormant state. The current work investigated the proteomic changes that <i>Mtb</i> undergoes in response to carbon starvation, a culture condition that models dormancy. The authors found broad effects of carbon starvation on the proteome, with the relative abundance of 37% of proteins significantly altered. Protein changes related to cell wall biosynthesis, metabolism, and drug susceptibility are discussed. Proteins associated with a carbon starvation phenotype are identified, and results are compared to other dormancy models, including hypoxia.