Exploring the targetome of IsrR, an iron-regulated sRNA controlling the synthesis of iron-containing proteins in Staphylococcus aureus

ABSTRACT: As integral parts of gene regulatory networks, small regulatory RNAs (sRNAs) play important roles in the adaptation of bacteria to environmental conditions. To adapt to iron limitation, many bacteria exploit an "iron-sparing" response mediated by Fur-regulated sRNAs such as RyhB of E. coli, allowing them to reduce the synthesis of iron-utilizing proteins not essential for growth. In this study, we aimed to confirm the regulatory role of the sRNA IsrR (Iron-sparing response Regulator) of S. aureus and to characterize the IsrR targetome in order to better understand the pathogens adaptation to iron-limited conditions often encountered in the host. To identify potential IsrR targets, two different experimental approaches were used. In the first, proteome profiles of S. aureus HG001 were compared to those of an isogenic ΔisrR mutant under iron-limited conditions. In the second approach, the effects of IsrR on the proteome under iron-rich conditions were analyzed using a strain in which IsrR was constitutively expressed from a plasmid. In silico target prediction was performed using the CopraRNA2 tool. Presence of IsrR caused a large number of consistent changes in protein levels both under iron-limited or iron-rich conditions. Among the proteins exhibiting significantly different abundance, 63 were in common between both experiments. Since sRNAs can have direct and indirect effects on global gene expression, the experimental approach was combined with in silico target prediction. In this way, very likely direct IsrR targets were identified, which include catalase (KatA) and three tricarboxylic acid (TCA) cycle enzymes (CitB, SdhA, SucA). Follow-up analyses confirmed that IsrR negatively affects KatA and CitB enzymatic activities. In contrast to most identified IsrR targets, the predicted interaction region of IsrR with the katA mRNA does not overlap the ribosome binding site, suggesting that IsrR cannot only inhibit translation, but also directly affect mRNA stability. A putative IsrR targetome was identified. In agreement with Fur-regulated sRNAs of other organisms, IsrR negatively affects the expression of TCA cycle and heme biosynthesis enzymes.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Staphylococcus Aureus

SUBMITTER: Larissa Busch  

LAB HEAD: Uwe Völker

PROVIDER: PXD045218 | Pride | 2024-07-12

REPOSITORIES: Pride