Bridging DNA contacts allow Dps from E. coli to condense DNA

Abstract

The DNA-binding protein from starved cells (Dps) plays a crucial role in maintaining bacterial cell viability during periods of stress. Dps is a nucleoid-associated protein that interacts with DNA to create biomolecular condensates in live bacteria. Purified Dps protein can also rapidly form large complexes when combined with DNA in vitro. However, the mechanism that allows these complexes to nucleate on DNA remains unclear. Here, we examine how DNA topology influences the formation of Dps-DNA complexes. We find that DNA supercoils offer the most preferred template for the nucleation of condensed Dps structures. More generally, bridging contacts between different regions of DNA can facilitate the nucleation of condensed Dps structures. In contrast, Dps shows little affinity for stretched linear DNA before it is relaxed. Once DNA is condensed, Dps forms a stable complex that can form inter-strand contacts with nearby DNA, even without free Dps present in solution. Taken together, our results establish the important role played by bridging contacts between DNA strands in nucleating and stabilizing Dps complexes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/576774v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1e4d842org.highwire.dtl.DTLVardef@131f3c6org.highwire.dtl.DTLVardef@7b6358org.highwire.dtl.DTLVardef@b73c32_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO Working model of nucleation and formation of Dps-DNA complex. Regions of supercoiled or stochastically bent DNA act as nucleation points for the formation of Dps-DNA complexes by allowing Dps to form bridging contacts. Dps does not readily bind to straight stretches of DNA in isolation. Once Dps-DNA complexes are formed they can form bridging contacts to bind additional DNA. C_FIG