Identification and structural characterization of novel bacteriocins by genome-wide screening of hypothetical mini-proteins in Staphylococcus aureus

Bacteriocins are ribosomally synthesized small antimicrobial peptides secreted by bacteria to overcome colonization resistance from closely related competitive microorganisms. Staphylococcus aureus is an opportunistic pathogen, that colonizes the skin and nasal cavity of healthy individuals and causes both superficial and systemic infections. The bacteriocins are the primary tool of S. aureus to compete with other members of the human microbiota for effective colonization. Different S. aureus strains produce various bacteriocins with widely diverse target organisms, which are mostly unexplored. Identification of new bacteriocins and their target organism can help us to understand the ecology of the S. aureus infection and lead to finding better treatment. Moreover, bacteriocins can help in the alternative treatment of antibiotic-resistant infections as well as have major applications in food preservation and agriculture. A large section of the S. aureus genome encodes small proteins consisting of 100 or fewer amino acids called mini-proteins. Analyzing the amino acid sequence of the hypothetical mini-proteins for the co-occurrence of antimicrobial activity and signal for extracellular secretion, seven novel bacteriocins genes are identified from S. aureus NCTC 8325. Newly identified bacteriocin genes are found to have stress and starvation inducible upstream regulatory elements, which upregulate bacteriocin production in nutrient-limited or colonization-resistant induced stress environments. The identified peptides have a high net positive charge, which facilitates interaction with negatively charged bacterial membranes. Ab initio modeling of the peptides, molecular dynamic simulation and structural comparison with known AMPs identified structural elements important for membrane disruption and bactericidal activity.