The iron-regulated small regulatory RNA IsrR modulates expression of genes utilized for dioxygen metabolism and heme synthesis in Staphylococcus aureus

ABSTRACT Bacterial regulatory RNAs (sRNAs) are commonly short non-coding RNAs that function as pleiotropic regulators by post-transcriptionally impacting mRNA stability and/or translation. They play significant roles in bacterial physiology and are typically expressed in response to specific environmental stimuli such as nutrient limitation. The bacterial pathogen Staphylococcus aureus faces decreased access to essential metal ions, including iron, in the mammalian host via a process called nutritional immunity. In response to host-mediated iron limitation, S. aureus expresses the sRNA IsrR, which coordinates an iron-sparing response by downregulating the expression of mRNAs coding for iron-requiring proteins or processes. Herein, we utilized MS2-Affinity Purification coupled with RNA Sequencing (MAPS) to reveal the in vivo IsrR interaction network. Analysis of co-purified RNAs revealed previously unpredicted putative IsrR targets coding for proteins associated with iron-requiring processes. We validated that IsrR directly interacts with nine targets in vitro . We demonstrate physiological roles for IsrR in mediating heme biosynthesis, aerobic respiration, and the detoxification of oxygen radicals. These activities are critical for pathogenesis, and this study establishes how S. aureus leverages these processes to adapt to iron scarcity, which is commonly encountered in the mammalian host. IMPORTANCE Staphylococcus aureus causes numerous and varied infections in mammals, making it a significant public health burden and concern. The prevalence of S. aureus infections is due to its robust repertoire of virulence factors and its ability to adapt to host microenvironments. Elucidation of the metabolic processes and pathways that promote adaptation to host-promoted stressors provides information about host-pathogen interactions. It could also aid the development of new antimicrobials or unveil treatment and prevention strategies. One common stress bacteria encounter within the mammalian hosts is limited access to iron. In response to iron scarcity, S. aureus expresses the regulatory sRNA IsrR. Here, we identified mRNAs that associate with IsrR. We verified that IsrR targets mRNAs that code for proteins involved in aerobic respiration, the metabolism of reactive oxygen species, and heme synthesis. This work provides significant insight into how S. aureus responds to host-mediated iron starvation.