Molecular mechanism of albicidin-dependent transcription activation by the antibiotic resistance factor AlbA

The escalating spread of antimicrobial resistance demands antibiotics with novel mechanisms of action. Albicidin is a potent DNA gyrase inhibitor produced by Xanthomonas species, and bacteria counter its activity through resistance mechanisms including the albicidin-sequestering protein AlbA from Klebsiella oxytoca. AlbA is a MerR family transcription activator that binds albicidin and stimulates expression of the albA gene, but how ligand recognition is coupled to transcription activation has remained unclear. Here, we use cryogenic electron microscopy and complementary biochemical assays to define the mechanism of AlbA-dependent transcription activation. Structures of transcription complexes reveal that AlbA remodels the promoter, repositioning the -35 element for productive sigma70 recognition and RNA polymerase engagement. Albicidin does not measurably alter AlbAs DNA affinity or the architecture of the mature open complex. Instead, transcription kinetics and experiments bypassing promoter opening indicate that albicidin selectively facilitates a promoter opening-dependent transition. AlbA is released upon synthesis of approximately five nucleotides, concomitant with downstream DNA melting, bubble translocation and upstream DNA rewinding rather than DNA scrunching. Together, these findings establish a sequential mechanism in which AlbA remodels promoter architecture, while albicidin tunes the kinetic transition to promoter opening, linking antibiotic recognition to induction of its sequestration machinery.