Antimicrobial drug discovery through bacteriophage genomics

Abstract

Over evolutionary time bacteriophages have developed unique proteins that arrest critical cellular processes to commit bacterial host metabolism to phage reproduction. Here, we apply this concept of phage-mediated bacterial growth inhibition to antibiotic discovery. We sequenced 26 Staphylococcus aureus phages and identified 31 novel polypeptide families that inhibited growth upon expression in S. aureus. The cellular targets for some of these polypeptides were identified and several were shown to be essential components of the host DNA replication and transcription machineries. The interaction between a prototypic pair, ORF104 of phage 77 and DnaI, the putative helicase loader of S. aureus, was then used to screen for small molecule inhibitors. Several compounds were subsequently found to inhibit both bacterial growth and DNA synthesis. Our results suggest that mimicking the growth-inhibitory effect of phage polypeptides by a chemical compound, coupled with the plethora of phages on earth, will yield new antibiotics to combat infectious diseases.

Characterization of temperate phage Che12 and construction of a new tool for diagnosis of tuberculosis

“…22 The approach using genomics of temperate phages of Staphylococcus aureus has been employed to identify phage ORFs with antimicrobial activity and their cognate bacterial targets for subsequent drug discovery. 25 In 1998, Yoon et al, 26 used temperate phages for Cre/loxP-mediated excision and amplification of large segments of the E. coli genome. Shimizu-Kadota (2001) 27 , reported the stability of the final integrant, in the bacterial chromosome for up to 50 generations in Lactobacilli signifying the robustness of the temperate phages.…”

Fluorescence Correlation Spectroscopy To Study Diffusion and Reaction of Bacteriophages inside Biofilms

“…Accumulated data from sequence analyses indicate that up to 20% of each bacterial genome may consist of phage-related DNA (8). The importance of these phage-related sequences to bacterial evolution is more striking in the context of lysogenic conversion (e.g., when numerous bacterial toxins are encoded by converting prophages) (32).…”

“…The emergence of pathogenic bacteria resistant to antimicrobial agents has highlighted the need for alternative means to treat human and animal bacterial infections. In this context, there are new prospects for phage therapy in the form of the application or ingestion of phage particles as an alternative to antibiotics (1,11,14,21,32,35,41,48,51). A recent major breakthrough for phage therapy was the approval by the U.S. Food and Drug Administration of a cocktail of bacteriophages as a treatment for Listeria monocytogenes contamination in ready-to-eat meat and poultry products (5).…”

The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages

“…Lytic bacteriophages have shown clinical promise as therapeutic agents for topical or systemic treatments of bacterial infections (11) or for their ability to block and subvert essential host metabolic pathways (12). The latter point makes them attractive tools to discover and validate essential bacterial genes targeted during the phage replicative cycle.…”