DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius

Abstract

In archaeal microorganisms, the compaction and organization of the chromosome into a dynamic but condensed structure is mediated by diverse chromatin-organizing proteins in a lineage-specific manner. While many archaea employ eukaryotic-type histones for nucleoid organization, this is not the case for the crenarchaeal model species <i>Sulfolobus acidocaldarius</i> and related species in Sulfolobales, in which the organization appears to be mostly reliant on the action of small basic DNA-binding proteins. There is still a lack of a full understanding of the involved proteins and their functioning. Here, a combination of in vitro and in vivo methodologies is used to study the DNA-binding properties of Sul12a, an uncharacterized small basic protein conserved in several Sulfolobales species displaying a winged helix-turn-helix structural motif and annotated as a transcription factor. Genome-wide chromatin immunoprecipitation and target-specific electrophoretic mobility shift assays demonstrate that Sul12a of <i>S. acidocaldarius</i> interacts with DNA in a non-sequence specific manner, while atomic force microscopy imaging of Sul12a-DNA complexes indicate that the protein induces structural effects on the DNA template. Based on these results, and <i>a contrario</i> to its initial annotation, it can be concluded that Sul12a is a novel chromatin-organizing protein.