Poly-γ-L-diaminobutanoic Acid Degrading Enzyme Serves as a Self-Resistance Mechanism to Protect Bacillus pumilus from Inhibition by Its Own Products

Poly-γ-L-diaminobutanoic acid (γ-PAB) is an antibiotic produced by marine bacteria Bacillus pumilus, showing considerable potential for applications in the fields of food, agriculture, and animal husbandry. The γ-PAB synthetase (Pas) and the γ-PAB-degrading enzyme (Pad) coexist within the cell. To enhance the γ-PAB fermentation production, this study utilized homologous recombination to delete the pad gene of Pad, creating a mutant strain Δpad. The validation of fermentation, achieved through pH adjustments, produced the following findings: (1) γ-PAB yield of Δpad significantly decreased to only 11.2% of that of the parent strain B. pumilus GS3-M7, instead of increasing; (2) by adjusting the pH to 5.5, GS3-M7 completely degraded the accumulated γ-PAB within 6 h, while the γ-PAB concentration in Δpad strain’s culture medium remained unchanged. This indicates the presence of only one type of Pad in B. pumilus and that the Δpad strain lost its degrading activity; (3) analysis of intracellular products and key enzyme activities revealed that the physiological metabolism of Δpad strain was suppressed under γ-PAB stress, and oxidative damage was notably higher compared to GS3-M7; (4) transcriptomic analysis identified 1726 differentially expressed genes (DEGs), in which genes related to oxidation–reduction processes, cationic antimicrobial peptide resistance, and peptidoglycan biosynthesis were significantly upregulated, whereas genes associated with ribosome, macromolecule biosynthesis, TCA cycle, and biosynthesis of various antibiotics were significantly downregulated. These findings demonstrate that Pad in B. pumilus functions as a self-resistance mechanism by degrading intracellular excess γ-PAB, thereby preventing autoinhibition by its own antimicrobial product. This represents a novel subclass of chemical modification mechanisms.