Ribosome hibernation in zinc-starved Mycobacterium abscessus confers amikacin tolerance

Intrinsic and acquired antibiotic resistance in Mycobacterium abscessus present unique challenges in treatment of its infections, which are rapidly emerging as a significant public health threat. The majority of clinically relevant antibiotics used against M. abscessus infections target the ribosome, which undergoes remodeling and hibernation in Mycobacterium smegmatis and Mycobacterium tuberculosis in response to zinc-limiting conditions. Ribosome remodeling involves replacement of multiple zinc-binding C+ ribosomal proteins with a CXXC motif by their respective C- paralogs lacking the motif, whereas ribosome hibernation involves recruitment of mycobacterial protein Y (Mpy) to the mRNA decoding center on the 30S subunit. Here, we report that zinc-responsive ribosome remodeling and hibernation are conserved in M. abscessus. We further demonstrate that Mpy binding suppresses translation and preserves ribosome abundance under zinc-limited conditions, while conferring tolerance to the aminoglycoside amikacin. Systematic biochemical analyses demonstrate that amino acid residues of Mpy that are critical for its interaction with the ribosome are also essential for Mpy stability in the cytosol. Together, these findings demonstrate amikacin tolerance as an important outcome of ribosome hibernation in M. abscessus.

Mycobacterium abscessus causes life-threatening infections in people with underlying health conditions. The treatment regimens for M. abscessus infections are months-long and include several ribosome-targeting antibiotics, such as amikacin. The long regimens are primarily attributed to intrinsic drug resistance in the pathogen. However, mechanisms of resistance for several of the antibiotics remain unclear. Here, we show that ribosome hibernation in M. abscessus by Mpy under zinc-starved conditions, which likely prevail in hosts, is a key determinant of amikacin tolerance. Thus, Mpy is a potential target for potentiating amikacin activity against M. abscessus.