Deciphering the Role of pafBC in Mycobacteriophage Resistance and Biofilm Formation

Tuberculosis (TB) remains the world's deadliest bacterial infection, with 8.2 million newly notified cases and an estimated 1.25 million deaths in 2023. Alarmingly, ∼19% of multidrug- or rifampicin-resistant (MDR/RR) strains already meet the World Health Organization (WHO) definition of pre-XDR-TB because they are resistant to at least one fluoroquinolone (FQ). Although gyrA/gyrB target-site mutations dominate clinical FQ resistance, Mycobacteria also rely on transcriptional networks that help them withstand the oxidative and DNA strand-breaking stress caused by these drugs. Central to this response is the heterodimeric transcription factor pafBC, whose WYL domain binds to single-stranded DNA and redirects RNA polymerase to a dedicated promoter set, thereby orchestrating a LexA-independent DNA-damage response (DDR). Up-regulation of pafBC has been linked to enhanced intracellular survival of M. tuberculosis and nontuberculous mycobacteria after FQ exposure, yet the downstream phenotypes and their connection to drug or phage resistance have remained unclear. Here, we demonstrate that deletion of pafBC in Mycobacterium smegmatis profoundly remodels the cell envelope, as evidenced by altered colony rugosity, reduced sliding motility, enhanced aggregation, and a three- to 5-fold decline in quantitative biofilm biomass. Untargeted lipid profiling revealed the selective depletion of long-chain trehalose polyphosphates and other apolar glycolipids that normally decorate the outer membrane─lipid classes that have recently been shown in other studies to serve as essential receptors for therapeutic mycobacteriophages such as BPs and Muddy. Consistent with this lipid deficit, the pafBC mutant exhibited markedly reduced phage adsorption and plaque formation; ectopic expression of RecA restored adsorption efficiency, implicating DDR envelope crosstalk in antiphage defense. Complementation with wild-type pafBC rescued lipid composition, biofilm mass, and phage resistance, whereas a WYL-domain mutant that cannot bind single-stranded DNA failed to do so, underscoring the necessity of canonical pafBC activation for envelope homeostasis. Immunoprofiling in THP-1 macrophages further showed that pafBC-proficient bacilli induce significantly higher secretion of IL-1β, TNF-α, and IL-6 compared to their isogenic mutant. This effect correlated with the presence of intact surface glycolipids, molecules known to interact with scavenger and Toll-like receptors on phagocytes and to enhance opsonizing antibody deposition at the host-pathogen interface. Overall, our findings connect the molecular mechanisms of the pafBC DDR with observable phenotypes such as fluoroquinolone tolerance, biofilm structure, phage resistance, and host immune recognition, by highlighting cell-envelope remodeling as the central factor.