Bacterial Heterochromatin Formation Through Liquid-Liquid Phase Separation

Heterochromatin is most often associated with eukaryotic organisms. Yet, bacteria also contain areas with densely protein-occupied chromatin that silences gene expression. One nucleoid-associated silencing factor is Hfq, which is strongly enriched at prophages and mobile genetic elements. Here we demonstrate that polyphosphate, an ancient and highly conserved polyanion, is essential for the specific binding of Hfq to these regions. Lack of either polyphosphate or Hfq causes unsolicited prophage and transposon mobilization, which drastically increases mutagenesis. We discovered that Hfq and polyphosphate form high molecular weight complexes that interact with DNA in phase-separated viscous condensates. We propose that polyP provides a scaffold that promotes Hfq binding to DNA regions with high intrinsic curvature, and thus serves as one hitherto unknown driver of heterochromatin formation in bacteria. Overall design: We present two major types of data here: First, a series of RNA-seq samples comparing the behavior of WT and ppk E. coli cells, either under basal growth or in the presence of cisplatin treatment (overall 2-4 replicates for each of three conditions for each genotype). Second, a series of ChIP-seq samples tracking the location of Hfq binding to the chromosome of wild type vs. ppk cells (3 genotypes, 2 replicates per genotype for ChIP and 2 replicates per genotype for matched input samples)