ABCF protein-mediated resistance shapes bacterial responses to antibiotics based on their type and concentration

ABCF-ATPases are increasingly recognized as translation factors that rescue stalled ribosomes when they encounter difficult mRNA templates or are stalled by antibiotics. The latter defines antibiotic resistance ABCF (ARE ABCF) proteins, known for their role in antibiotic resistance. However, in this study, we reveal a broader role of ARE ABCFs in antibiotic-responsive regulation. Using genetic, OMICs, and biochemical approaches, we showed that ARE ABCF proteins TiaA and Are5sc in Streptomyces coelicolor use their resistance functions to modulate specialized metabolism and proteosynthesis in response to lincosamide, streptogramin A, and pleuromutilin (LS_AP) antibiotics. Although under LS_AP exposure, either Are5sc or TiaA is essential for activating the biosynthesis of the redox-active antimicrobial actinorhodin, these proteins exhibit distinct functions at the proteome level, defined by their resistance profiles and temporally regulated expression. Are5sc facilitates early adaptive responses by modulating the WblC regulon across a broad range of LS_AP concentrations, while TiaA is induced later, specifically at higher concentrations, where it suppresses antibiotic stress responses, particularly against pleuromutilins. TiaA function thus reflects the ecological context of LS_AP antibiotics as pleuromutilins are produced by fungi, whereas lincosamides/streptogramins originate from actinomycetes. Our findings demonstrate that ARE ABCF proteins, through their resistance function, act as global regulators of translation, mirroring the roles of non-ARE ABCF proteins like EttA. This highlights their broader ecological and physiological significance, extending beyond their established role in antibiotic resistance.

Bacteria adapt to diverse stimuli mainly through transcriptional changes that regulate adaptive protein factors. Here, we show that responses to protein synthesis-inhibiting antibiotics are fine-tuned by antibiotic resistance ABCF proteins at the translational level, enabling bacteria to differentiate between antibiotic classes and concentrations for a tailored response. Additionally, we have demonstrated that these proteins can specialize in conferring high-level resistance to specific antibiotics. Given their prevalence in pathogenic bacteria, antibiotic resistance ABCF (ARE ABCF) proteins may play a crucial role in resistance development, particularly against new antibiotics targeting the ribosomal catalytic center, presenting a significant challenge for antimicrobial therapy.