A significant scientific milestone has been achieved by Prof. Dr. Ayten Yazgan-Karataş and her team at Istanbul Technical University with their recent publication in Annals of Microbiology, titled "The direct regulatory effects of Bacilysin on the cellular physiology of Bacillus subtilis". This study, which reveals the antibiotic bacilysin’s complex role as a global signaling molecule, has received extraordinary acclaim from Nobel Laureate Sir John E. Walker. In a personal congratulatory email, Sir Walker—who won the Nobel Prize in Chemistry—remarked that it was "gratifying" to see research on bacilysin, which was the subject of his own doctoral thesis, reach such a "sophisticated level of understanding." This direct validation from a Nobel Laureate not only honors Dr. Karataş’s sophisticated contribution to microbiology but also highlights the global impact of her team's research in decoding the multilayered regulatory networks of bacteria.

Bacilysin is a small dipeptide antibiotic produced by Bacillus subtilis and several other Bacillus species. Although extensively studied for its antimicrobial activity, its role as a potential intracellular regulatory molecule has not been well characterized. This study presents the first comprehensive transcriptomic evaluation of bacilysin’s direct effects on B. subtilis physiology, highlighting its influence on metabolic regulation, developmental pathways, and stress responses.

To examine these regulatory effects, bacilysin was purified from a producing B. subtilis PY79 strain, separated by RP-HPLC, and structurally confirmed with UPLC-MS (m/z 271.14 [M+H]⁺). Exponentially growing B. subtilis cells (OD₆₀₀ ~0.8) were exposed to sub-lethal concentrations of the purified compound. Following treatment, RNA-Seq analysis was performed to compare transcriptomes of bacilysin-treated cells with untreated controls. Differential expression analysis revealed 121 significantly altered genes, including 60 upregulated and 61 downregulated transcripts. Notably, 98 of these genes had never previously been linked to bacilysin exposure, demonstrating the novelty of the regulatory landscape uncovered.

Functional categorization of the differentially expressed genes indicated that bacilysin disrupts or modulates several global regulatory networks. These networks include carbon catabolite  control (CcpA), nitrogen metabolism via CodY and TnrA, and multicellular behaviors controlled by the DegS/DegU two-component system. Bacilysin treatment induced changes in genes associated with carbohydrate utilization, amino-acid and nitrogen metabolism, and transport systems, suggesting that the compound interferes with nutrient-dependent regulatory circuits. Interestingly, antagonistic patterns emerged between bacilysin-responsive genes and those normally controlled by CodY and CcpA, implying that bacilysin may act as a metabolic or environmental signal that alters hierarchical nutrient-sensing pathways.

Beyond metabolism, bacilysin exposure influenced developmental processes such as sporulation and germination. Several genes involved in the early stages of sporulation were differentially regulated, indicating that bacilysin may signal cellular stress or resource limitation. Additionally, genes associated with biofilm formation and swarming motility were altered, suggesting possible effects on community behavior. These findings support the idea that bacilysin indirectly shapes population dynamics by modulating multicellular traits.

Another key finding relates to metal and ion homeostasis. Genes involved in zinc transport and protein-metal interactions exhibited significant changes, demonstrating that bacilysin perturbs intracellular metal balance. This effect could be linked to its known ability to inhibit enzymes through interference with amino-acid metabolism.

Importantly, bacilysin also appears to regulate its own biosynthetic operon, contributing to a potential positive feedback mechanism that amplifies production under certain physiological conditions. Moreover, interactions with the srfA operon (surfactin synthesis) and the signaling gene phrC suggest coordination between antibiotic production, quorum sensing, and multicellular behavior.

Collectively, the study reveals that bacilysin functions not only as an antimicrobial molecule but also as a signaling metabolite capable of reprogramming gene expression in B. subtilis. This dual role highlights its importance in microbial ecology, competition, and adaptation. The work opens new avenues for investigating bacilysin-mediated regulatory pathways and exploring its potential applications in biotechnology, microbial engineering, and biological control strategies.

https://doi.org/10.1186/s13213-025-01813-x