The Lrs14-like AbfR1 homolog from Metallosphaera sedula is a nucleoid-organizing protein

ChIP-seq analysis of the Lrs14 protein AbfR1 from Metallosphaera sedula (Msed_2175)

Nucleoid organization in Crenarchaeota is mediated by a plethora of diverse families of small DNA-binding proteins. However, the role of the Lrs14 family, a prevalent family of small DNA-binding proteins within the Crenarchaeal order of the Sulfolobales, remained rather ambiguous. Previous studies have focused on gene regulatory functions of the Lrs14 family and have shown that the Lrs14-type protein AbfR1 is involved in the regulation of biofilm formation and motility in the model species Sulfolobus acidocaldarius. In this study, we set out to investigate the DNA-binding characteristics of the AbfR1 homolog in Metallosphaera sedula, a related mixotrophic species within Crenarchaeota. AbfR1Ms and AbfR1Sa share 50% amino acid sequence identity and are structurally very similar. We observed that heterologously purified AbfR1Ms forms dimers in solution and binds DNA in vitro in a non-sequence-specific manner with diverse DNA probes. Chromatin immunoprecipitation in combination with high-throughput sequencing revealed an association of AbfR1Ms with numerous sites across the genome of Metallosphaera sedula. This genome-wide association was found to correlate with AT-rich regions and possibly with the global chromatin structure, rather than with specific DNA sequences. Notably, the most highly enriched AbfR1Ms binding sites were characterized by extended DNA regions spanning several thousand base pairs. Atomic force microscopy further demonstrated that AbfR1Ms promotes DNA condensation and aggregation, suggesting a role in chromatin architecture. These findings suggest that AbfR1Ms, and possibly other related Lrs14 members, play a critical role in nucleoid organization, with properties resembling those of bacterial nucleoid-associated proteins.