Carbon starvation of Mycobacterium abscessus induces a non-replicating state with extensive proteomic remodeling

Mycobacterium abscessus (Mab) is an opportunistic pathogen that can cause chronic, debilitating lung disease. Mab is intrinsically resistant to most antibiotics, making Mab infections challenging to manage and frequently incurable. During infection, Mab adapts to survive various stresses, including hypoxia and nutrient starvation. In vitro, these conditions drive Mab into a drug-tolerant, non-replicating state. Changes in the Mab proteome that result from entering a non-replicating state have been minimally described despite the clinical importance of this physiological state. Using Mab reference strain ATCC 19977, we collected proteomic data comparing replicating to non-replicating states using a carbon starvation (CS) model of persistence. We identified 2,251 proteins overall (45% proteome coverage), and 17% of these proteins were found in only one of the two conditions. A third of identified proteins were significantly changed in abundance, indicating an extensive proteomic response to CS. The response regulator DosR and many DosRS-responsive proteins were significantly more abundant under CS, suggesting that this response regulator plays a key role in CS-induced Mab persistence. Many aspects of cell wall biosynthesis were altered, including changes in glycolipid abundance under CS. Proteins involved in other key cellular processes such as secretion, oxidative phosphorylation, and nutrient metabolism were altered under CS. This proteomic analysis provides new insights and clarity into how the Mab proteome is regulated during non-replicating persistence, a key consideration for understanding Mab pathophysiology.IMPORTANCEMycobacterium abscessus (Mab) is a highly drug-resistant species of non-tuberculous mycobacteria (NTM). People most susceptible to pulmonary NTM infections are immunocompromised or have an existing lung disease, such as chronic obstructive pulmonary disease or cystic fibrosis. Infections with Mab cause chronic lung disease that is challenging to manage. Patients typically must take multiple antibiotics daily for at least a year. Despite aggressive treatment regimens, cure rates remain low. One reason for this is Mab's ability to enter dormancy during chronic infections. The authors provide a first description of the proteomic remodeling that occurs in Mab in response to carbon starvation, which induces a non-replicating state. They report that a third of the proteome changes in response to carbon starvation, including pathways involved in cell envelope biosynthesis, energy production, and nutrient acquisition. The detailed description of these changes provides insights into the adaptations likely used by Mab to survive during infection.