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. How different family members contribute to chromatin structuring, and the interplay between them, is not fully understood. More specifically, the role of the Lrs14 family, a prevalent family of small DNA-binding proteins within Crenarchaeota, 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. We observed that heterologously purified AbfR1Ms forms dimers in solution and binds DNA in vitro in a non-sequence-specific manner upon testing diverse DNA probes. Chromatin immunoprecipitation in combination with high-throughput sequencing revealed a widespread association of AbfR1Ms with 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, high-enrichment sites represented an association with extended DNA regions spanning several thousand base pairs. Atomic force microscopy (AFM) 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.