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Antimicrobial drug discovery through bacteriophage genomics


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.

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We thank M. Virta for providing us with the pTOO21 vector and C.Y. Lee for vectors used in essentiality analysis. We thank all PhageTech technical staff for their assistance during the course of this research. We also would like to thank the National Research Council (Canada) Industrial Research Assistance Program for their support of part of our research. J.L., M.D., M.C., N.H., T.K., G.M. and R.S. are recipients of the Natural Sciences and Engineering Research Council of Canada Industrial Research Fellowship.

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Correspondence to Jing Liu.

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All the authors are/were employed or compensated by PhageTech, which owns the intellectual property related to the work reported in this paper.

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Figure 1: Functional screening for growth-inhibitory polypeptides encoded by phage 77.
Figure 2: Interaction of 77ORF104 and S. aureus DnaI.
Figure 3: dnaI essentiality analysis.
Figure 4: Effects of phage inhibitory ORF expression on metabolic pathways.