Small RNA IsrR mediates the staphylococcal response to iron limitation

Staphylococcus aureus has evolved mechanisms to cope with low iron (Fe) availability in host tissues. S. aureus uses the ferric uptake transcriptional regulator (Fur) to sense titers of cytosolic Fe. Upon Fe depletion, apo-Fur relieves transcriptional repression of genes utilized for Fe uptake. We demonstrate that an S. aureus Δfur mutant has decreased expression of acnA, which codes for the Fe-dependent enzyme aconitase. This prevents the Δfur mutant from growing with amino acids as sole carbon and energy sources. We used a suppressor screen to exploit this phenotype and determined that a mutation that decreases the transcription of isrR, which produces a regulatory RNA, increased acnA expression, thereby enabling growth. Directed mutation of bases predicted to facilitate the interaction between the acnA transcript and IsrR, decreased the ability of IsrR to control acnA expression in vivo and IsrR bound to the acnA transcript in vitro. IsrR also bound transcripts coding the alternate TCA cycle proteins sdhC, mqo, citZ, and citM. MS2-Affinity Purification followed by RNA Sequencing revealed the IsrR targetome included transcripts coding for proteins involved in heme biosynthesis, aerobic respiration and the oxidative stress response. Using reporter fusions, we demonstrate a role for IsrR in promoting the transcription of S. aureus virulence factor expression. Results support a model where upon Fe scarcity, isrR is expressed and controls iron homeostasis and impacts bacterial pathogenesis.