Mining and Statistical Modeling of Natural and Variant Class IIa Bacteriocins Elucidate Activity and Selectivity Profiles across Species

• Published in: Applied and environmental microbiology 2020-10, Vol.86 (22)
• Main Authors: Tresnak, Daniel T, Hackel, Benjamin J
• Format: Article
• Language: English
• Subjects: Antibiotic resistance; Antibiotics; Antiinfectives and antibacterials; Antimicrobial activity; Antimicrobial agents; Antimicrobial peptides; Bacteriocins; Bacteriocins - metabolism; Chymotrypsin; Enterococcus - drug effects; Enterococcus - metabolism; Enzymology and Protein Engineering; Gene Library; Genes, Bacterial; Genomes; In vivo methods and tests; Listeria; Listeria - drug effects; Listeria - metabolism; Mannose; Mathematical models; Membrane composition; Pepsin; Peptides; Phosphotransferase; Pore Forming Cytotoxic Proteins - metabolism; Proteolysis; Selectivity; Stability analysis; Statistical analysis; Statistical models; Strains (organisms); Trypsin; Vancomycin
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.01646-20

Class IIa bacteriocin antimicrobial peptides (AMPs) are a compelling alternative to current antimicrobials because of potential specific activity toward antibiotic-resistant bacteria, including vancomycin-resistant enterococci. Engineering of these molecules would be enhanced by a better understanding of AMP sequence-activity relationships to improve efficacy and limit effects of off-target activity. Toward this goal, we experimentally evaluated 210 natural and variant class IIa bacteriocins for antimicrobial activity against six strains of enterococci. Inhibitory activity was ridge regressed to AMP sequence to predict performance, achieving an area under the curve of 0.70 and demonstrating the potential of statistical models for identifying and designing AMPs. Active AMPs were individually produced and evaluated against eight enterococcus strains and four strains to elucidate trends in susceptibility. It was determined that the mannose phosphotransferase system (manPTS) sequence is informative of susceptibility to class IIa bacteriocins, yet other factors, such as membrane composition, also contribute strongly to susceptibility. A broadly potent bacteriocin variant (lactocin DT1) from a genome was identified as the only variant with inhibitory activity toward all tested strains, while a novel enterocin variant (DT2) from an genome demonstrated specificity toward strains. Eight AMPs were evaluated for proteolytic stability to trypsin, chymotrypsin, and pepsin, and three C-terminal disulfide-containing variants, including divercin V41, were identified as compelling for future studies, given their high potency and proteolytic stability. Class IIa bacteriocin antimicrobial peptides (AMPs), an alternative to traditional small-molecule antibiotics, are capable of selective activity toward various Gram-positive bacteria, limiting negative side effects associated with broad-spectrum activity. This selective activity is achieved through targeting of the mannose phosphotransferase system (manPTS) of a subset of Gram-positive bacteria, although factors affecting this mechanism are not entirely understood. Peptides identified from genomic data, as well as variants of previously characterized AMPs, can offer insight into how peptide sequence affects activity and selectivity. The experimental methods presented here identify promising potent and selective bacteriocins for further evaluation, highlight the potential of simple computational modeling for prediction of AMP