Abstract
Ref is an HNH superfamily endonuclease that only cleaves DNA to which RecA protein is bound. The enigmatic physiological function of this unusual enzyme is defined here. Lysogenization by bacteriophage P1 renders E. coli more sensitive to the DNA-damaging antibiotic ciprofloxacin, an example of a phenomenon termed phage-antibiotic synergy (PAS). The complementary effect of phage P1 is uniquely traced to the P1-encoded gene ref. Ref is a P1 function that amplifies the lytic cycle under conditions when the bacterial SOS response is induced due to DNA damage. The effect of Ref is multifaceted. DNA binding by Ref interferes with normal DNA metabolism, and the nuclease activity of Ref enhances genome degradation. Ref also inhibits cell division independently of the SOS response. Ref gene expression is toxic to E. coli in the absence of other P1 functions, both alone and in combination with antibiotics. The RecA proteins of human pathogens Neisseria gonorrhoeae and Staphylococcus aureus serve as cofactors for Ref-mediated DNA cleavage. Ref is especially toxic during the bacterial SOS response and the limited growth of stationary phase cultures, targeting aspects of bacterial physiology that are closely associated with the development of bacterial pathogen persistence.
Highlights
As multidrug resistance in important bacterial pathogens becomes an ever more serious health crisis [1], a need for new therapeutic strategies is evident [2,3,4,5]
The bacteriophage P1-encoded Ref protein is a novel class of endonuclease, cleaving only DNA to which the bacterial RecA protein is bound
We define Ref as a P1 function that amplifies the lytic cycle under conditions when the bacterial SOS response is induced due to DNA damage
Summary
As multidrug resistance in important bacterial pathogens becomes an ever more serious health crisis [1], a need for new therapeutic strategies is evident [2,3,4,5]. Phage therapy is slowly advancing as an approach to improve food safety, enhance water quality, provide an alternative to antibiotics in food-producing animals, facilitate environmental biocontrol of multidrug resistant pathogens on surfaces in hospitals, and treat wounds in humans [7]. Phage therapy may prove useful, not just as an alternative to antibiotics, and as a complement. Phage-antibiotic synergy or PAS—has been noted in multiple reports involving a variety of bacterial species [10,11,12,13,14,15]. The degrees of complementarity vary, the phenomenon does not typically reflect synergy in the genetic sense; i.e., where the effects of the phage and antibiotic are reliably greater than additive. The overall result is a complementation of antibiotic action by phage in reducing bacterial survival
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