StIA is a Novel Nucleoid-Associated Protein of Streptococcus pneumoniae that Activates DNA Topoisomerase I

Abstract

Topoisomerases are essential enzymes that maintain DNA topology. The activity of some of these enzymes is regulated by protein cofactors. Here, we identify a previously uncharacterized nucleoid-associated protein from the human pathogen Streptococcus pneumoniae that binds double-stranded DNA (dsDNA) in a sequence-independent manner both in vitro and in vivo and activates topoisomerase I (Topo I). This protein was named StIA (Streptococcal Topoisomerase I Activator). In vivo analyses showed that deletion of stIA impairs bacterial growth in the presence of the Topo I inhibitor seconeolitsine, whereas its overproduction decreases susceptibility to this compound. Consistent with these observations, StIA specifically stimulates Topo I activity without affecting DNA gyrase. StIA forms oligomers and assembles into higher-order nucleoprotein complexes upon DNA-binding. Mechanistic analyses revealed that StIA does not alter DNA cleavage by Topo I but specifically enhances the DNA religation step of its catalytic cycle. This activation is likely mediated through a direct protein-protein interaction, as StIA and Topo I physically associate in vitro. Structural modeling further supports the formation of a StIA-Topo I complex and identifies putative contact residues involved in the interaction. Collectively, these findings establish StIA as a novel nucleoid-associated with a dual function: promoting nucleoprotein complex assembly and stimulating Topo I activity through direct interaction with the enzyme. More broadly, our results suggest that the regulation of topoisomerase activity by accessory proteins may represent an important mechanism for fine-tuning DNA topological homeostasis and could provide new opportunities for the development of antibacterial therapies.