Building blocks and blueprints for bacterial autolysins

Bacteria utilize a wide variety of endogenous cell wall hydrolases, or autolysins, to remodel their cell walls during processes including cell division, biofilm formation, and programmed death. We here systematically investigate the composition of these enzymes in order to gain insights into their associated biological processes, potential ways to disrupt them via chemotherapeutics, and strategies by which they might be leveraged as recombinant antibacterial biotherapies. To do so, we developed LEDGOs (lytic enzyme domains grouped by organism), a pipeline to create and analyze databases of autolytic enzyme sequences, constituent domain annotations, and architectural patterns of multi-domain enzymes that integrate peptidoglycan binding and degrading functions. We applied LEDGOs to eight pathogenic bacteria, gram negatives Acinetobacter baumannii, Klebsiella pneumoniae, Neisseria gonorrhoeae, and Pseudomonas aeruginosa; and gram positives Clostridioides difficile, Enterococcus faecium, Staphylococcus aureus, and Streptococcus pneumoniae. Our analysis of the autolytic enzyme repertoires of these pathogens reveals commonalities and differences in their key domain building blocks and architectures, including correlations and preferred orders among domains in multi-domain enzymes, repetitions of homologous binding domains with potentially complementarity recognition modalities, and sequence similarity patterns indicative of potential divergence of functional specificity among related domains. We have further identified a variety of unannotated sequence regions within the lytic enzymes that may themselves contain new domains with important functions. Author summary Bacteria use enzymes called autolysins to remodel their cell walls, for example during cell division and formation of biofilms. We have developed a bioinformatics pipeline to analyze the autolysin repertoires of a number of different pathogenic bacteria, comparing and contrasting the domain building blocks from which their autolysins are constructed, the amino acid sequence diversity of the domains, and the architectural patterns by which the domains are assembled into complete enzymes. Our analysis provides insights into important biological processes, indicates sequences that would likely benefit from experimental characterization, highlights potential targets for chemotherapeutic intervention, and even suggests strategies for building next-generation autolysin biotherapies that turn a pathogen's own proteins against it to destroy its cell wall.

Automated summary

This study systematically investigates the role of bacterial autolysins in biological processes and developed a pipeline to analyze the autolysin repertoires of various pathogenic bacteria, revealing commonalities and differences among them. Furthermore, unannotated sequence regions within the lytic enzymes were identified, which may contain new domains with important functions.