MACROMOLECULAR CROWDING EFFECTS ON THE INTERACTION OF DNA WITH ESCHERICHIA-COLI DNA-BINDING PROTEINS - A MODEL FOR BACTERIAL NUCLEOID STABILIZATION

DNA-binding protein fractions from exponential and stationary phase ce ll extracts of E. coli were isolated by affinity chromatography on nat ive DNA-cellulose. The ability of these fractions to convert DNA into a readily-sedimented form was compared in the absence or presence of a dded polymers. In the absence of polymers, large amounts of the protei ns were required. In the presence of polyethylene glycol or polyvinylp yrrolidone, much smaller amounts of the DNA-binding proteins were requ ired, indicating a macromolecular crowding effect from these polymers. The enhanced binding under crowded conditions appears to resolve a pa radox between the cellular abundance of the DNA-binding proteins and t he amounts required in earlier in vitro studies. The 'histone-like' pr otein HU from the DNA-binding protein fraction was preferentially inco rporated into the pelleted DNA in the presence of polymers. Purified H U at roughly similar amounts caused a similar conversion of DNA to a r eadily-sedimentable ('condensed') form. Crowding-enhancement of DNA co ndensation by promoting the binding of proteins to the DNA provides a model for the stabilization of systems such as the bacterial nucleoid or kinetoplast DNA.