The Nucleoid Occlusion Protein SlmA Binds to Lipid Membranes

Abstract

Protection of the chromosome from scission by the division machinery during cytokinesis is critical for bacterial survival and fitness. This is achieved by nucleoid occlusion, which, in conjunction with other mechanisms, ensures formation of the division ring at midcell. In Escherichia coli, this mechanism is mediated by SlmA, a specific DNA binding protein that antagonizes assembly of the central division protein FtsZ into a productive ring in the vicinity of the chromosome. Here, we provide evidence supporting direct interaction of SlmA with lipid membranes, tuned by its binding partners FtsZ and SlmA binding sites (SBS) on chromosomal DNA. Reconstructions in minimal membrane systems that mimic cellular environments show that SlmA binds to lipid-coated microbeads or locates at the edge of microfluidic-generated microdroplets, inside which the protein is encapsulated. DNA fragments containing SBS sequences do not seem to be recruited to the membrane by SlmA but instead compete with SlmA’s ability to bind lipids. The interaction of SlmA with FtsZ modulates this behavior, ultimately triggering membrane localization of the SBS sequences alongside the two proteins. The ability of SlmA to bind lipids uncovered in this work extends the interaction network of this multivalent regulator beyond its well-known protein and nucleic acid recognition, which may have implications in the overall spatiotemporal control of division ring assembly. IMPORTANCE Successful bacterial proliferation relies on the spatial and temporal precision of cytokinesis and its regulation by systems that protect the integrity of the nucleoid. In Escherichia coli, one of these protectors is SlmA protein, which binds to specific DNA sites around the nucleoid and helps to shield the nucleoid from inappropriate bisection by the cell division septum. Here, we discovered that SlmA not only interacts with the nucleoid and septum-associated cell division proteins but also binds directly to cytomimetic lipid membranes, adding a novel putative mechanism for regulating the local activity of these cell division proteins. We find that interaction between SlmA and lipid membranes is regulated by SlmA’s DNA binding sites and protein binding partners as well as chemical conditions, suggesting that the SlmA-membrane interactions are important for fine-tuning the regulation of nucleoid integrity during cytokinesis.

Lipid Surfaces and Glutamate Anions Enhance Formation of Dynamic Biomolecular Condensates Containing Bacterial Cell Division Protein FtsZ and Its DNA-Bound Regulator SlmA

“…Previous results have shown that FtsZ·SlmA·SBS condensates accumulate at the lipid interface when encapsulated in lipid-stabilized microdroplets . Interestingly, SlmA binds to lipid membranes, as recently revealed by biochemical membrane-reconstitution approaches . These findings suggest that membrane surfaces may control biomolecular phase separation in bacteria, as shown already in several eukaryotic systems, and may help to modulate FtsZ spatiotemporal organization inside bacterial cells.…”

Studying Nucleoid-Associated Protein–DNA Interactions Using Polymer Microgels as Synthetic Mimics

“…Although in vitro studies, including investigations of SBS-SlmA interaction, , are often performed in chloride salts, changing from potassium chloride to potassium glutamate can enhance the protein–DNA interaction in vitro by stabilizing protein–DNA complexes . In addition, glutamate as anion is also physiologically more relevant .…”

Min waves without MinC can pattern FtsA-anchored FtsZ filaments on model membranes

“…For example, nucleoid occlusion and other unknown factors may assist in positioning cell division. SlmA, bound directly to lipid membranes and DNA, could play a role in the spatiotemporal modulation of Z-ring assembly by narrowing the division site at midcell 59 .…”